From dmb at mrc-dunn.cam.ac.uk Thu Jan 1 13:28:42 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 1 Jan 2004 18:28:42 -0000 (GMT) Subject: bio-basket (was RE: [BiO BB] how to access database remotely) In-Reply-To: References: Message-ID: <33522.80.1.204.145.1072981722.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- > Hi Dan, > >> I like the 'shopping basket' approach to bio data analysis. > > Would you like to elaborate a little bit on this design approach? I am not sure how implementation details will pan out, but I imagine an 'object basket' which we can carry between different pages and manipulate in various ways as we go. As the concrete details are a little shaky, here is an example use case to illustrate what I have in mind. 1) Issue a query via the web interface for bacterial transporters (for example). 2) Dump the results in our basket as 'sequence objects'. Now we want to know a bit more about the contents of the basket. 3) Navigate to a 'sequence clustering' page or a 'family database' page to discover how many distinct families of bacterial transporter we have. 4) Add the family objects to the basket. The family objects act over the sequence objects in a 'sensible way' as well as carrying additional (family specific) information. For example each family may encompass a much broader superset of sequences not annotated as bacterial transporters. 5) Remove some stray families from the basket. 6) etc, etc. I think by adding code to the basket as well as data we allow different web service designers to integrate in a much more flexible way - but this is still shaky. For example, someone could build a website to visualize a 'sequence alignment' object, and carrying our basket to that page (after somehow acquiring alignment objects (we dont care how)) we can see our data. Depending on the complexity of the site we may be able to perform visual queries over our basket, before taking analysis further. As you can see this isn't an original idea, but I think the basket is a nice way for people to feel like they have hold of something. Everything can take place over the WWW and the basket itself can return a list of actions performed on its contents. This 'action list' could then be printed, saved or exported to the web as a new unary 'basket function' itself. I love the idea that any analysis published in bioinformatics could be repeated by any interested party in this way. I feel this is a bit more 'open' than the SRS type system, and allows more 'sensible' integration more easily than other systems. However, we are talking serious computer science technology under the hood. The basket itself is where all the integration takes place, and so the objects it contains (data objects or analysis objects) should have configuration interfaces to allow this to be fine tuned by the user (not hidden from him). Cheers, Dan. From B.A.T.Svensson at lumc.nl Fri Jan 2 10:26:08 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 2 Jan 2004 16:26:08 +0100 Subject: bio-basket (was RE: [BiO BB] how to access database remotely) Message-ID: > I feel this is a bit more 'open' than the SRS type system, > and allows more 'sensible' integration more easily than > other systems. SRS is what came to my mind when I read the first part of your answer. But your ideas seams (or rather have a good potential) to be much more user friendly than the SRS standard layout, which has, in my oppinion, a to high learning treshhold level. > However, we are talking serious computer > science technology under the hood. What do you have in mind here? From dmb at mrc-dunn.cam.ac.uk Sat Jan 3 14:43:54 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 3 Jan 2004 19:43:54 -0000 (GMT) Subject: bio-basket (was RE: [BiO BB] how to access database remotely) In-Reply-To: References: Message-ID: <32827.80.1.204.145.1073159034.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- > > I feel this is a bit more 'open' than the SRS type system, >> and allows more 'sensible' integration more easily than >> other systems. > > SRS is what came to my mind when I read the first part of your answer. But your > ideas seams (or rather have a good potential) to be much more user friendly than > the SRS standard layout, which has, in my oppinion, a to high learning treshhold > level. > >> However, we are talking serious computer >> science technology under the hood. > > What do you have in mind here? That is the $64,000 question! Lets see what comes out of DILS04 > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From B.A.T.Svensson at lumc.nl Sat Jan 3 16:48:34 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Sat, 3 Jan 2004 22:48:34 +0100 Subject: bio-basket (was RE: [BiO BB] how to access database remotely) Message-ID: >>> However, we are talking serious computer >>> science technology under the hood. >> >> What do you have in mind here? > That is the $64,000 question! > Lets see what comes out of DILS04 May I very humbly suggest something? From dmb at mrc-dunn.cam.ac.uk Sat Jan 3 18:03:36 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 3 Jan 2004 23:03:36 -0000 (GMT) Subject: bio-basket (was RE: [BiO BB] how to access database remotely) In-Reply-To: References: Message-ID: <32826.80.1.204.145.1073171016.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- > >>>> However, we are talking serious computer >>>> science technology under the hood. >>> >>> What do you have in mind here? > >> That is the $64,000 question! > >> Lets see what comes out of DILS04 > > May I very humbly suggest something? Fire away! I am more than happy to discuss any and all possibilities! :) From B.A.T.Svensson at lumc.nl Sat Jan 3 19:09:55 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Sun, 4 Jan 2004 01:09:55 +0100 Subject: bio-basket (was RE: [BiO BB] how to access database remotely) Message-ID: >>>>> However, we are talking serious computer >>>>> science technology under the hood. >>>> >>>> What do you have in mind here? >> >>> That is the $64,000 question! >> >>> Lets see what comes out of DILS04 >> >> May I very humbly suggest something? >Fire away! I am more than happy to discuss any and all possibilities! > >:) Keep it (read: the data model) simple. From dmb at mrc-dunn.cam.ac.uk Sat Jan 3 19:22:02 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sun, 4 Jan 2004 00:22:02 -0000 (GMT) Subject: bio-basket (was RE: [BiO BB] how to access database remotely) In-Reply-To: References: Message-ID: <34037.80.1.204.145.1073175722.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- > >>>>>> However, we are talking serious computer >>>>>> science technology under the hood. >>>>> >>>>> What do you have in mind here? >>> >>>> That is the $64,000 question! >>> >>>> Lets see what comes out of DILS04 >>> >>> May I very humbly suggest something? > > >>Fire away! I am more than happy to discuss any and all possibilities! >> >>:) > > Keep it (read: the data model) simple. I agree :) However there are always more complex data models to deal with. Every time you do science you are data modelling. The trick is to stay within your domain when it comes to the details, and step up to a higher level representation to get more perspective where necessary. From pankaj at nii.res.in Tue Jan 6 10:35:11 2004 From: pankaj at nii.res.in (Pankaj) Date: Tue, 06 Jan 2004 21:05:11 +0530 (IST) Subject: [BiO BB] hi Message-ID: hi all, i m a new member of this board. i have a 3 protein structures (all taking the same fold) with the substrate bound. the residues surrounding the substrate are the active site residues. now i have a set of 400 protein sequences which i know take the same above mentioned fold. i want to extract the active site residues from these 400 sequences. but whatever alignment program i use either uses only sequence information or only structure information. is there an alignment program which can use both structure and sequence information for the alignment of these 400 sequences on the strcutural template From pac at bcm.tmc.edu Tue Jan 6 11:25:40 2004 From: pac at bcm.tmc.edu (BCM HUMAN RESOURCES) Date: Tue, 6 Jan 2004 10:25:40 -0600 (CST) Subject: [BiO BB] hi Message-ID: <200401061625.KAA17495@cuda.corp.bcm.tmc.edu> This user is no longer with Baylor College of Medicine. Thanks, Baylor College of Medicine From gary at www.bioinformatics.org Tue Jan 6 11:48:53 2004 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Tue, 6 Jan 2004 11:48:53 -0500 (EST) Subject: [BiO BB] hi In-Reply-To: Message-ID: Hi Pankaj, I know of a commercial software product than can combines structure and sequence information to do mulitple alignments: MOE, developed by the chemical computing group. I think they have educational versions available for a reduced cost, or maybe even free. Try: http://www.chemcomp.com/ They a have an article available on their alignment algorithm: http://www.chemcomp.com/Journal_of_CCG/Features/align.htm Hope that helps. Regards, g. On Tue, 6 Jan 2004, Pankaj wrote: > hi all, > i m a new member of this board. > i have a 3 protein structures (all taking the same fold) with the > substrate bound. the residues surrounding the substrate are the active > site residues. now i have a set of 400 protein sequences which i know > take the same above mentioned fold. i want to extract the active site > residues from these 400 sequences. but whatever alignment program i > use either uses only sequence information or only structure > information. is there an alignment program which can use both > structure and sequence information for the alignment of these 400 > sequences on the strcutural template > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From rong at bu.edu Tue Jan 6 12:30:55 2004 From: rong at bu.edu (Rong Chen) Date: Tue, 6 Jan 2004 12:30:55 -0500 (EST) Subject: [BiO BB] hi In-Reply-To: Message-ID: Hi Pankaj, DS Protein Family in DS Modeling may be helpful. Check this web site: http://www.accelrys.com/dstudio/ds_modeling/. Rong On Tue, 6 Jan 2004, Pankaj wrote: > hi all, > i m a new member of this board. > i have a 3 protein structures (all taking the same fold) with the > substrate bound. the residues surrounding the substrate are the active > site residues. now i have a set of 400 protein sequences which i know > take the same above mentioned fold. i want to extract the active site > residues from these 400 sequences. but whatever alignment program i > use either uses only sequence information or only structure > information. is there an alignment program which can use both > structure and sequence information for the alignment of these 400 > sequences on the strcutural template > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From landman at scalableinformatics.com Thu Jan 8 11:25:16 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Thu, 08 Jan 2004 11:25:16 -0500 Subject: [BiO BB] need a good pedagogical overview Message-ID: <1073579116.5035.61.camel@protein.scalableinformatics.com> Hi Folks: I have been asked to find pointers to a good and accessible walk through of the informatics computing market, needs, etc. Is anyone aware of such a document or presentation somewhere? I am not talking about an IDC or similar research report, rather something that describes the problems, the issues, etc. and is accessible to a non-scientist (e.g. low on jargon). Please let me know if you are aware of something like this. I would prefer to avoid (re)writing this. Thanks in advance! Joe -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From sravan_111 at rediffmail.com Thu Jan 8 23:00:37 2004 From: sravan_111 at rediffmail.com (sravan sravan) Date: 9 Jan 2004 04:00:37 -0000 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #601 - 3 msgs Message-ID: <20040109040037.18056.qmail@webmail31.rediffmail.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- Hello everybody, I am working with secondary structure alignments. In order to optimize the gap penalties for the alignment of secondary structure strings with dynamic programming mehtod, I am using the following method. 1. Selecting of N number of pairs of proteins(each pair is a set of two structurally similar / sequence similarity: 70<%id<100) ). 2. secondary structure generation of the chains per pair. 3. Running the alignments of each pair with N combinations of gap penalties.(structure specific). 4. At wchich combination various proteins give highest structure alignment(sst aligns) with the paired one than with the others(low scores), that combination can be selected. queries::: ----------- 00) I am trying to select the similar pairs from FSSP table given by DALI. (TABLE2.html). In this pairs given in table I wanted to select the unique pairs based on a criteria (rmsd,%Id).. CAN I SELECT A PAIR WITH SEQ %ID: 70<%ID<100? WHAT SHOULD BE THE VALUE OF RMSD? (01) ANY IMPROVEMENTS TO THE METHOD I AM THINKING? (01)ANY OTHER METHODLOGY TO OPTIMISE THE GAP PENALTIES FOR SECONDARY STRUCTURE ALIGNMENT? Thank you all for the co operation. Regards. P.Sravana Kumar. From dmb at mrc-dunn.cam.ac.uk Fri Jan 9 04:26:45 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 9 Jan 2004 09:26:45 -0000 (GMT) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #601 - 3 msgs In-Reply-To: <20040109040037.18056.qmail@webmail31.rediffmail.com> References: <20040109040037.18056.qmail@webmail31.rediffmail.com> Message-ID: <51405.193.60.81.207.1073640405.squirrel@www.mrc-dunn.cam.ac.uk> ++ sravan sravan-- > > Hello everybody, >         I am working with secondary structure alignments. In > order to optimize the gap penalties for the alignment of secondary structure > strings with dynamic programming mehtod, I am using the following method.   >     1. Selecting of N number of pairs of proteins(each pair is a set of > two structurally similar / sequence similarity: 70<%id<100) ).     >   2. secondary structure generation of the chains per pair.     >   3. Running the alignments of each pair with N combinations of gap > penalties.(structure specific).       4. At wchich combination > various proteins give highest structure alignment(sst aligns) with the paired one > than with the others(low scores), that combination can be selected. queries::: > ----------- > 00) I am trying to select the similar pairs from FSSP table given by DALI. > (TABLE2.html). In this pairs given in table I wanted to select the unique pairs > based on a criteria (rmsd,%Id).. >       CAN I SELECT A PAIR WITH SEQ %ID: 70<%ID<100? WHAT > SHOULD BE THE VALUE OF RMSD? I would get all sequences in a fold then compare sequence identity, then pick pairs from within the fold which match your criteria. > (01) ANY IMPROVEMENTS TO THE METHOD I AM THINKING? 70% sequence identity is very high! - > (01)ANY OTHER METHODLOGY TO OPTIMISE THE GAP PENALTIES FOR SECONDARY STRUCTURE > ALIGNMENT? Probably many you could think of (i.e. counting the gaps between homologus pairs of SS in structures), but none that I know of. > > Thank you all for the co operation. Cheers! > Regards. > P.Sravana Kumar. > From pankaj at nii.res.in Fri Jan 9 05:20:32 2004 From: pankaj at nii.res.in (Pankaj) Date: Fri, 09 Jan 2004 15:50:32 +0530 (IST) Subject: [BiO BB] redundant data Message-ID: hi everybody, i have a set for 200 sequences where the sequence similarity varies between 28-90%. i want to select a representative set from this bigger set so that i pick up sequences which are representative of the whole set. ie from this bigger set i want to remove the sequences that are very similar and represent them by just a single sequence. ie i want to have a non redundant set. can anyone please tell how thanx in advance pankaj From dmb at mrc-dunn.cam.ac.uk Fri Jan 9 06:28:03 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 9 Jan 2004 11:28:03 -0000 (GMT) Subject: [BiO BB] redundant data In-Reply-To: <58092.193.60.81.207.1073645827.squirrel@www.mrc-dunn.cam.ac.uk> References: <58092.193.60.81.207.1073645827.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <51472.193.60.81.207.1073647683.squirrel@www.mrc-dunn.cam.ac.uk> ++ Pankaj-- > hi everybody, > i have a set for 200 sequences where the sequence similarity varies between > 28-90%. i want to select a representative set from this bigger set so that i pick > up sequences which are representative of the whole set. ie from this bigger set i > want to remove the sequences that are very similar and represent them by just a > single sequence. ie i want to have a non redundant set. can anyone please tell how > thanx in advance > pankaj One of the very quickest (and also easiest) ways to do this is using the excellent program cd-hit ... http://bioinformatics.ljcrf.edu/cd-hi/ It should run in a couple of seconds for 200 sequences. I have some perl scripts to parse the output into mysql (tab delimited) for easy cluster analysis if you like. There are a couple of small problems with this software which the author is aware of but is too busy to fix. It would be nice to make this a project to develop the software here. Alternatively you can use blastclust, which does what its name suggests, but has an extra 'coverage' parameter which is not explicitly present in cd-hit. It is slower, but on 200 sequences it will still finish in around 1 min. Also blastclust allows an arbitary sequence identity threshold for clustering, whereas cd-hit is limited to a minimum of 40% identity. On bigger sequence sets (>5,000) the fundamental differences between blastclust and cd-hit make cd-hit a good choice. With all sequence clustering algorithms you have to worry about 'the domain problem', but I am not sure which technique currenly deals with this the best. I know of one algorithm (DIVCLUS) which was explicitly designed to handle this problem, Park J, Teichmann SA. DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics. 1998;14(2):144-50. http://bioinformatics.oupjournals.org/cgi/pmidlookup?view=reprint&pmid=9545446 Ta, Dan. > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From moyc at mail.med.upenn.edu Fri Jan 9 12:58:49 2004 From: moyc at mail.med.upenn.edu (Chris Moy) Date: Fri, 9 Jan 2004 12:58:49 -0500 Subject: [BiO BB] Code available for microRNAs Message-ID: <7A1332AF-42CD-11D8-B2F7-000A9599E70C@mail.med.upenn.edu> Hello, I started a project about a year ago and it does not look like I will be able to complete it. I was starting to build a database of precursor miRNAs for the mouse and human genome by walking through the genome and bending back small sections of the genome back on itself. I have also built an alignment tool to align a sequence to the precursor database. The code is written in perl and is little old and inefficient but they seem to work pretty well. If anyone is interested in using it please let me know. It is ideal for building a miRNA database on a cluster. Chris From combiofriends at yahoo.com Fri Jan 9 13:08:15 2004 From: combiofriends at yahoo.com (com bio) Date: Fri, 9 Jan 2004 10:08:15 -0800 (PST) Subject: [BiO BB] perl-web Message-ID: <20040109180815.17373.qmail@web20728.mail.yahoo.com> i have a web page. when some one visits it , it asks for his name. i would like to capture the name he enters using a variable in PERL. how do i go about? deepan chakravarthy n ===== ------------------------------------------- center for biotehnology anna university chennai-25 india __________________________________ Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus From joel.dudley at asu.edu Fri Jan 9 13:16:33 2004 From: joel.dudley at asu.edu (Joel Dudley) Date: Fri, 9 Jan 2004 11:16:33 -0700 Subject: [BiO BB] perl-web In-Reply-To: <20040109180815.17373.qmail@web20728.mail.yahoo.com> References: <20040109180815.17373.qmail@web20728.mail.yahoo.com> Message-ID: I don't see how this is related to bioinformatics. Head over to www.perl.org to find the solution to your problem. On Jan 9, 2004, at 11:08 AM, com bio wrote: > i have a web page. > when some one visits it , it asks for his name. > i would like to capture the name he enters using a > variable in PERL. how do i go about? > deepan chakravarthy n > > ===== > ------------------------------------------- > center for biotehnology > anna university > chennai-25 > india > > __________________________________ > Do you Yahoo!? > Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes > http://hotjobs.sweepstakes.yahoo.com/signingbonus > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From merlyn at stonehenge.com Fri Jan 9 13:16:39 2004 From: merlyn at stonehenge.com (Randal L. Schwartz) Date: 09 Jan 2004 10:16:39 -0800 Subject: [BiO BB] Re: [PBML] perl-web In-Reply-To: <20040109180815.17373.qmail@web20728.mail.yahoo.com> References: <20040109180815.17373.qmail@web20728.mail.yahoo.com> Message-ID: <86isjlrnqw.fsf@blue.stonehenge.com> >>>>> "com" == com bio writes: com> i have a web page. com> when some one visits it , it asks for his name. com> i would like to capture the name he enters using a com> variable in PERL. how do i go about? That would be writing a web form with a "form" element, and having the "action" of the form point at a URL triggering a Perl script, most likely in CGI mode. The CGI module is your friend here. "perldoc CGI" for the details, or read any of the millions of documents written in the past decade. Welcome to the web. You are programmer number 4,982,129. :) -- Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095 Perl/Unix/security consulting, Technical writing, Comedy, etc. etc. See PerlTraining.Stonehenge.com for onsite and open-enrollment Perl training! From hamid at ibb.ut.ac.ir Fri Jan 9 14:08:37 2004 From: hamid at ibb.ut.ac.ir (Hamid Nikbakht) Date: Fri, 09 Jan 2004 22:38:37 +0330 Subject: [BiO BB] Code available for microRNAs In-Reply-To: <7A1332AF-42CD-11D8-B2F7-000A9599E70C@mail.med.upenn.edu> Message-ID: <20040109191121.C35EFD28E9@www.bioinformatics.org> Dear Chris, Tell me more about your code and project, recently I've finished my project on alpha helices and now I'm studying to start a new project. you can see one of my last project on all secondary structures of globular proteins as a database. An article is now going to be prepared in a short time. you can visit it here: http://www.ibc.ut.ac.ir/pssd/ I would be great for me if you would let me know more about your project and database. Maybe we can finish this database project and have an article on it. ?------------------------------------------------ | Hamid Nikbakht, ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?| | M.Sc of Cell and Molecular Biology, ? ? ? ? ? ?| | Laboratory of Biophysics and Molecular Biology,| | Institute of Biochemistry and Biophysics(IBB), | | University of Tehran, ? ? ? ? ? ? ? ? ? ? ? ? ?| | Tehran,Iran. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | | Tel: +98-21-611-3322 ? ? ? ? ? ? ? ? ? ? ? ? ? | | Fax: +98-21-640-4680 ? ? ? ? ? ? ? ? ? ? ? ? ? | | E-Mail: hamid at ibb.ut.ac.ir ? ? ? ? ? ? ? ? ? ? | | Alt. E-mail: nikbakht at ibb.ut.ac.ir ? ? ? ? ? ? | ?------------------------------------------------ From prathibha_562 at yahoo.co.in Mon Jan 12 05:32:21 2004 From: prathibha_562 at yahoo.co.in (=?iso-8859-1?q?prathibha=20bharathi?=) Date: Mon, 12 Jan 2004 10:32:21 +0000 (GMT) Subject: [BiO BB] How to calculate smithwaterman and z-scores while performing local alignment using smith-waterman algo.. In-Reply-To: <20040109180815.17373.qmail@web20728.mail.yahoo.com> Message-ID: <20040112103221.32585.qmail@web8205.mail.in.yahoo.com> Hi, can any body of you suggest me how to calculate z-score and smith-waterman score while performing local alignment using smith-waterman algorithm. ThankYou Prathibha com bio wrote: i have a web page. when some one visits it , it asks for his name. i would like to capture the name he enters using a variable in PERL. how do i go about? deepan chakravarthy n ===== ------------------------------------------- center for biotehnology anna university chennai-25 india __________________________________ Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Yahoo! India Mobile: Ringtones, Wallpapers, Picture Messages and more.Download now. -------------- next part -------------- An HTML attachment was scrubbed... URL: From amaldeep75 at hotmail.com Sat Jan 10 16:46:30 2004 From: amaldeep75 at hotmail.com (amal) Date: Sun, 11 Jan 2004 03:16:30 +0530 Subject: [BiO BB] How to calculate smithwaterman and z-scores while performing local alignment using smith-waterman algo.. References: <20040112103221.32585.qmail@web8205.mail.in.yahoo.com> Message-ID: put the z-dscore in the array of the matrix of the smith and then divide by the waterman and then align the algo . ----- Original Message ----- From: prathibha bharathi To: bio_bulletin_board at bioinformatics.org Sent: Monday, January 12, 2004 4:02 PM Subject: [BiO BB] How to calculate smithwaterman and z-scores while performing local alignment using smith-waterman algo.. Hi, can any body of you suggest me how to calculate z-score and smith-waterman score while performing local alignment using smith-waterman algorithm. ThankYou Prathibha com bio wrote: i have a web page. when some one visits it , it asks for his name. i would like to capture the name he enters using a variable in PERL. how do i go about? deepan chakravarthy n ===== ------------------------------------------- center for biotehnology anna university chennai-25 india __________________________________ Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Yahoo! India Mobile: Ringtones, Wallpapers, Picture Messages and more. Download now. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ngadewal at yahoo.com Wed Jan 14 06:34:39 2004 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 14 Jan 2004 03:34:39 -0800 (PST) Subject: [BiO BB] comparison tool Message-ID: <20040114113439.35776.qmail@web40903.mail.yahoo.com> Dear Members, Any software or tool available to compare the scan image of normal skin (normal.jpeg) with scan image of disease skin (disease.jpeg) under standard parameters. Thanks in advance. regards, Nikhil --------------------------------- Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes -------------- next part -------------- An HTML attachment was scrubbed... URL: From basm101 at york.ac.uk Wed Jan 14 12:20:15 2004 From: basm101 at york.ac.uk (Bryony) Date: Wed, 14 Jan 2004 17:20:15 +0000 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #607 - 1 msg References: <20040114170113.2D2D2D2A36@www.bioinformatics.org> Message-ID: <40057A4F.1050501@york.ac.uk> Try Matlab basm101 bio_bulletin_board-request at bioinformatics.org wrote: >When replying, PLEASE edit your Subject line so it is more specific >than "Re: BiO_Bulletin_Board digest, Vol..." And, PLEASE delete any >unrelated text from the body. > > >Today's Topics: > > 1. comparison tool (nikhil gadewal) > >--__--__-- > >Message: 1 >Date: Wed, 14 Jan 2004 03:34:39 -0800 (PST) >From: nikhil gadewal >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] comparison tool >Reply-To: bio_bulletin_board at bioinformatics.org > >--0-904315790-1074080079=:33196 >Content-Type: text/plain; charset=us-ascii > >Dear Members, > >Any software or tool available to compare the scan image of normal skin (normal.jpeg) with scan image of disease skin (disease.jpeg) under standard parameters. > >Thanks in advance. > >regards, >Nikhil > > >--------------------------------- >Do you Yahoo!? >Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes >--0-904315790-1074080079=:33196 >Content-Type: text/html; charset=us-ascii > >
Dear Members,
>
 
>
Any software or tool available to compare the scan image of normal skin (normal.jpeg) with scan image of disease skin (disease.jpeg) under standard parameters.
>
 
>
Thanks in advance.
>
 
>
regards,
>
Nikhil


>Do you Yahoo!?
>Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes >--0-904315790-1074080079=:33196-- > > >--__--__-- > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >End of BiO_Bulletin_Board Digest > > From valery at biozak.com Wed Jan 14 14:53:00 2004 From: valery at biozak.com (Valery Miftakhov) Date: Wed, 14 Jan 2004 11:53:00 -0800 Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? References: <20040114170116.7C0D0D2AA1@www.bioinformatics.org> Message-ID: <40059E1C.7020507@biozak.com> Dear Bioinformatics Gurus, This is Valery Miftakhov from BioXelera, Inc. We are building affordable hardware accelerators for various bioinformatics algorithms (BLAST, Smith-Waterman, HMM, NAMD). Our misison is to enable individual researchers and small labs to speed up their research and level the playing field with the 'big guys' who can afford throwing 100K per one acceleration module... We are currently refining our understanding of the number of users for each application and computing architectures they are running on. If anybody has some knowledge on this subject or some pointers to the right places, please contact me at valery at biozak.com of at the number below. Thank you very much in advance, -- Valery Miftakhov, Ph.D. -- (650)-906-0477 COO & VP, Business Development BioZak InfoBase, Inc. - Life Science Market Intelligence! From kucej at fns.uniba.sk Wed Jan 14 04:38:49 2004 From: kucej at fns.uniba.sk (Martin Kucej) Date: Wed, 14 Jan 2004 10:38:49 +0100 Subject: [BiO BB] Librarian 1.2 released Message-ID: <40051C39.3728.243D3A92@localhost> Librarian, a program, which enables a group of researchers to create an annotated virtual library of articles in portable document format (PDF) is now available in version 1.2. This release comes with several new features including renaming categories and journals, editing paper ratings, displaying MeSH suggestions for category creation, or abstract previews when hovering over Abstract links. Web form style of navigation was replaced by link tables, which are faster and better readable. Also, newly added articles are marked 'Today!' for easier identification. The older versions of Librarian (1.1, 1.1a) can be upgraded using 'Upgrade' release without reinstallation. http://bioinformatics.org/librarian/ Martin Kucej Department of Biochemistry Comenius University Mlynska dolina CH-1 Bratislava 84215 Slovak Republic From pankaj at nii.res.in Wed Jan 14 23:49:19 2004 From: pankaj at nii.res.in (Pankaj) Date: Thu, 15 Jan 2004 10:19:19 +0530 (IST) Subject: [BiO BB] struture viewing Message-ID: hello everyone, i have been using insightII (on SGI) for protein structure viewing and modelling of proteins and it seemed very friendly. now i have shifted to a linux machine on which insightII does not work. i have lot of options for macromolecular viewing tools (eg rasmol, vmd etc) for linux but i cannot decide which is the best. i tried rasmol but it was not very competent in terms that it didnt have many options. can someone help in this regard. thanks in advance pankaj From arunnuraa at rediffmail.com Thu Jan 15 00:59:57 2004 From: arunnuraa at rediffmail.com (Arun . A) Date: 15 Jan 2004 05:59:57 -0000 Subject: [BiO BB] struture viewing Message-ID: <20040115055957.19773.qmail@webmail27.rediffmail.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- Dear Pankaj Try for Swiss PDB Viewer. That is really good for Modelling. If that is not suitable for you, try for modeller. On Thu, 15 Jan 2004 Pankaj wrote : >hello everyone, >i have been using insightII (on SGI) for protein structure viewing and >modelling of proteins and it seemed very friendly. now i have shifted >to a linux machine on which insightII does not work. i have lot of >options for macromolecular viewing tools (eg rasmol, vmd etc) for >linux but i cannot decide which is the best. i tried rasmol but it was >not very competent in terms that it didnt have many options. can >someone help in this regard. >thanks in advance >pankaj From hamid at ibb.ut.ac.ir Thu Jan 15 01:18:56 2004 From: hamid at ibb.ut.ac.ir (Hamid Nikbakht) Date: Thu, 15 Jan 2004 09:48:56 +0330 Subject: [BiO BB] struture viewing In-Reply-To: Message-ID: <20040115061943.C9608D2335@www.bioinformatics.org> Hello, I strongly suggest WeblabViewer, I've forgotten its new name but if you search it you can find it. ?------------------------------------------------ | Hamid Nikbakht, ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?| | M.Sc of Cell and Molecular Biology, ? ? ? ? ? ?| | Laboratory of Biophysics and Molecular Biology,| | Institute of Biochemistry and Biophysics(IBB), | | University of Tehran, ? ? ? ? ? ? ? ? ? ? ? ? ?| | Tehran,Iran. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | | Tel: +98-21-611-3322 ? ? ? ? ? ? ? ? ? ? ? ? ? | | Fax: +98-21-640-4680 ? ? ? ? ? ? ? ? ? ? ? ? ? | | E-Mail: hamid at ibb.ut.ac.ir ? ? ? ? ? ? ? ? ? ? | | Alt. E-mail: nikbakht at ibb.ut.ac.ir ? ? ? ? ? ? | ?------------------------------------------------ -----Original Message----- From: Pankaj To: bio_bulletin_board at bioinformatics.org Date: Thu, 15 Jan 2004 10:19:19 +0530 (IST) Subject: [BiO BB] struture viewing > hello everyone, > i have been using insightII (on SGI) for protein structure viewing and > modelling of proteins and it seemed very friendly. now i have shifted > to a linux machine on which insightII does not work. i have lot of > options for macromolecular viewing tools (eg rasmol, vmd etc) for > linux but i cannot decide which is the best. i tried rasmol but it was > not very competent in terms that it didnt have many options. can > someone help in this regard. > thanks in advance > pankaj > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From bertrand.frottier at free.fr Thu Jan 15 08:58:58 2004 From: bertrand.frottier at free.fr (Bertrand FROTTIER) Date: Thu, 15 Jan 2004 08:58:58 -0500 Subject: [BiO BB] struture viewing In-Reply-To: References: Message-ID: <40069CA2.3020705@free.fr> Try VMD, it's a really impressive program, with many option, and scripting possibilities. http://www.ks.uiuc.edu/Research/vmd/ Pankaj a ?crit : > hello everyone, > i have been using insightII (on SGI) for protein structure viewing and > modelling of proteins and it seemed very friendly. now i have shifted > to a linux machine on which insightII does not work. i have lot of > options for macromolecular viewing tools (eg rasmol, vmd etc) for > linux but i cannot decide which is the best. i tried rasmol but it was > not very competent in terms that it didnt have many options. can > someone help in this regard. > thanks in advance > pankaj > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- () (o_ //\ <-V_/_ Demonic penguin "It's Choi." "Yeah. Yeah. You're two hours late." "I know, it's her fault." -- Choi and Neo, "The Matrix" From mynews at jtsmith2.us Thu Jan 15 09:44:56 2004 From: mynews at jtsmith2.us (James Smith) Date: Thu, 15 Jan 2004 09:44:56 -0500 Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <40059E1C.7020507@biozak.com> References: <20040114170116.7C0D0D2AA1@www.bioinformatics.org> <40059E1C.7020507@biozak.com> Message-ID: <4006A768.4060800@jtsmith2.us> An HTML attachment was scrubbed... URL: From cdwan at mail.ahc.umn.edu Thu Jan 15 10:01:13 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Thu, 15 Jan 2004 09:01:13 -0600 (CST) Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <4006A768.4060800@jtsmith2.us> References: <20040114170116.7C0D0D2AA1@www.bioinformatics.org> <40059E1C.7020507@biozak.com> <4006A768.4060800@jtsmith2.us> Message-ID: > Our misison is to enable individual researchers and small > labs to speed up their research and level the playing field > with the 'big guys' who can afford throwing 100K per one > acceleration module... My impression is that computational speed is the limiting factor for only a small number of groups. I think that most researchers remain interface and data management bound. I could be way off base with this, and I'm curious to hear about other experiences: I believe that (as is usually true with high performance computing) 5% of the researchers take up 95% of the cluster time, and the other 95% are doing the best they can to manage even a rather small set of results. Am I wrong? Are lots of people sitting on their hands waiting for BLAST (and HMMER, and InterPro, and meta-java-dock-o-matic-whatever) to complete? -Chris Dwan The University of Minnesota From dmb at mrc-dunn.cam.ac.uk Thu Jan 15 10:05:38 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 15 Jan 2004 15:05:38 -0000 (GMT) Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: References: <20040114170116.7C0D0D2AA1@www.bioinformatics.org> <40059E1C.7020507@biozak.com> <4006A768.4060800@jtsmith2.us> Message-ID: <56799.193.60.81.207.1074179138.squirrel@www.mrc-dunn.cam.ac.uk> ++ CCGB-- > >> Our misison is to enable individual researchers and small >> labs to speed up their research and level the playing field with the 'big >> guys' who can afford throwing 100K per one >> acceleration module... > > My impression is that computational speed is the limiting factor for only a small > number of groups. I think that most researchers remain interface and data > management bound. > > I could be way off base with this, and I'm curious to hear about other > experiences: I believe that (as is usually true with high performance computing) > 5% of the researchers take up 95% of the cluster time, and the other 95% are doing > the best they can to manage even a rather small set of results. > > Am I wrong? No you are not wrong, but perhaps we are just privilaged? Anyone want to borrow my idle time? Most of my time is scripting / debugging jobs to run. The machines sit idel most of the time, and finish in reasonable time for everything I need. I would be more likely to pay for a process pipeline manager - naturally I would preffer a free one. Any projects to make a process pipeline tool in php? Should - * allow workflows to be created / edited / monitored through web. * be tied into cron. * rely on gnu make under the hood. * be tied into cvs for 'job module' developement. * provide error reporting by mail. * provide log review. > Are lots of people sitting on their hands waiting for BLAST (and > HMMER, and InterPro, and meta-java-dock-o-matic-whatever) to > complete? > > -Chris Dwan > The University of Minnesota > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From mgollery at unr.edu Thu Jan 15 11:46:02 2004 From: mgollery at unr.edu (Martin Gollery) Date: Thu, 15 Jan 2004 08:46:02 -0800 Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <56799.193.60.81.207.1074179138.squirrel@www.mrc-dunn.cam.ac.uk> References: <20040114170116.7C0D0D2AA1@www.bioinformatics.org> <40059E1C.7020507@biozak.com> <4006A768.4060800@jtsmith2.us> <56799.193.60.81.207.1074179138.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <1074185162.4006c3ca74b43@webmail.unr.edu> Quoting Dan Bolser : > I would be more likely to pay for a process pipeline manager - naturally I > would > preffer a free one. > > Any projects to make a process pipeline tool in php? > > Should - > * allow workflows to be created / edited / monitored through web. > * be tied into cron. > * rely on gnu make under the hood. > * be tied into cvs for 'job module' developement. > * provide error reporting by mail. > * provide log review. Take a look at VIBE, from Incogen. It does quite a bit of what you want, and the Software Development Kit is free to non-commercial types. Marty Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From dmb at mrc-dunn.cam.ac.uk Thu Jan 15 13:57:33 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 15 Jan 2004 18:57:33 -0000 (GMT) Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <1074185162.4006c3ca74b43@webmail.unr.edu> References: <20040114170116.7C0D0D2AA1@www.bioinformatics.org> <40059E1C.7020507@biozak.com> <4006A768.4060800@jtsmith2.us> <56799.193.60.81.207.1074179138.squirrel@www.mrc-dunn.cam.ac.uk> <1074185162.4006c3ca74b43@webmail.unr.edu> Message-ID: <43305.193.60.81.207.1074193053.squirrel@www.mrc-dunn.cam.ac.uk> Thanks, I will have a look. Cheers, Dan. ++ Martin Gollery-- > Quoting Dan Bolser : > >> I would be more likely to pay for a process pipeline manager - naturally I would >> preffer a free one. >> >> Any projects to make a process pipeline tool in php? >> >> Should - >> * allow workflows to be created / edited / monitored through web. * be tied into >> cron. >> * rely on gnu make under the hood. >> * be tied into cvs for 'job module' developement. >> * provide error reporting by mail. >> * provide log review. > > Take a look at VIBE, from Incogen. It does quite a bit of what you want, and the > Software Development Kit is free to non-commercial types. > > Marty > > > Martin Gollery > Associate Director > Center For Bioinformatics > University of Nevada at Reno > Dept. of Biochemistry / MS330 > 775-784-7042 > > > ------------------------------------------------- > This mail sent through https://webmail.unr.edu > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From idoerg at burnham.org Fri Jan 16 00:50:35 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 15 Jan 2004 21:50:35 -0800 Subject: [BiO BB] struture viewing In-Reply-To: References: Message-ID: <40077BAB.10308@burnham.org> Hi Pankaj, I have always been partial to PyMol for visualization and terrific graphics. Swiss-PDB viewer is good on visualizatoin (not as great as PyMol), but adds modelling functionality, should you require it. People I know praise Molscipt for pulish-quality graphics. But I am not experienced with that. Hope this helps, Iddo Pankaj wrote: >hello everyone, >i have been using insightII (on SGI) for protein structure viewing and >modelling of proteins and it seemed very friendly. now i have shifted >to a linux machine on which insightII does not work. i have lot of >options for macromolecular viewing tools (eg rasmol, vmd etc) for >linux but i cannot decide which is the best. i tried rasmol but it was >not very competent in terms that it didnt have many options. can >someone help in this regard. >thanks in advance >pankaj >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 Tel: (858) 646 3100 x3516 Fax: (858) 646 3171 http://ffas.ljcrf.edu/~iddo From landman at scalableinformatics.com Fri Jan 16 00:55:53 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 16 Jan 2004 00:55:53 -0500 Subject: [BiO BB] struture viewing In-Reply-To: <40077BAB.10308@burnham.org> References: <40077BAB.10308@burnham.org> Message-ID: <40077CE9.1020803@scalableinformatics.com> I have been quite happy with VMD (http://www.ks.uiuc.edu), Ghemical, Pymol, and a few others. If you are an old XMol user, JMol will feel very familiar. There are quite a few others as well. Joe Iddo Friedberg wrote: > Hi Pankaj, > > I have always been partial to PyMol for visualization and terrific > graphics. Swiss-PDB viewer is good on visualizatoin (not as great as > PyMol), but adds modelling functionality, should you require it. > > People I know praise Molscipt for pulish-quality graphics. But I am > not experienced with that. > > Hope this helps, > > Iddo > > > Pankaj wrote: > >> hello everyone, >> i have been using insightII (on SGI) for protein structure viewing and >> modelling of proteins and it seemed very friendly. now i have shifted >> to a linux machine on which insightII does not work. i have lot of >> options for macromolecular viewing tools (eg rasmol, vmd etc) for >> linux but i cannot decide which is the best. i tried rasmol but it was >> not very competent in terms that it didnt have many options. can >> someone help in this regard. >> thanks in advance >> pankaj >> > -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From murphy at genome.chop.edu Fri Jan 16 13:56:30 2004 From: murphy at genome.chop.edu (Kevin Murphy) Date: Fri, 16 Jan 2004 13:56:30 -0500 Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <43305.193.60.81.207.1074193053.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: Dan, Let us know your experience, because I'm interested in what you describe also. I've always been interested in using make for things like this, and figured that we might roll our own system using perl, make, cvs, and RT (a GPL ticket-tracking system we use). Gotta run, in the background I hear somebody yelling something about a cold day in hell .... -Kevin On Thursday, January 15, 2004, at 01:57 PM, Dan Bolser wrote: > > Thanks, I will have a look. > > Cheers, > Dan. > > ++ Martin Gollery-- >> Quoting Dan Bolser : >> >>> I would be more likely to pay for a process pipeline manager - >>> naturally I would >>> preffer a free one. >>> >>> Any projects to make a process pipeline tool in php? >>> >>> Should - >>> * allow workflows to be created / edited / monitored through web. * >>> be tied into >>> cron. >>> * rely on gnu make under the hood. >>> * be tied into cvs for 'job module' developement. >>> * provide error reporting by mail. >>> * provide log review. >> >> Take a look at VIBE, from Incogen. It does quite a bit of what you >> want, and the >> Software Development Kit is free to non-commercial types. >> >> Marty From princess01232001 at rediffmail.com Sat Jan 17 03:27:54 2004 From: princess01232001 at rediffmail.com (Dhruti B Pathak) Date: 17 Jan 2004 08:27:54 -0000 Subject: [BiO BB] basic bioinformatics Message-ID: <20040117082754.31623.qmail@webmail30.rediffmail.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- hi everybody, What is bioinformatics What is the basic thing of bioinformatics How it helps in regular life What is its use thanks From princess01232001 at rediffmail.com Sat Jan 17 03:52:11 2004 From: princess01232001 at rediffmail.com (Dhruti B Pathak) Date: 17 Jan 2004 08:52:11 -0000 Subject: [BiO BB] about bioinformatics Message-ID: <20040117085211.3371.qmail@webmail6.rediffmail.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- hi friends I want some information about bioinformatics Means... What is the base of bioinformatics What it includes How it helpful to us Please send me information at princess01232001 at rediffmail.com Thanks u very much in advance From obj at obj.hopto.org Sat Jan 17 08:57:09 2004 From: obj at obj.hopto.org (Andrius) Date: Sat, 17 Jan 2004 15:57:09 +0200 Subject: [BiO BB] about bioinformatics In-Reply-To: <20040117085211.3371.qmail@webmail6.rediffmail.com> References: <20040117085211.3371.qmail@webmail6.rediffmail.com> Message-ID: <40093F35.7020101@obj.hopto.org> i think you can find precise and more detailed answers to these questions in the a web. just google. Dhruti B Pathak wrote: >hi friends > >I want some information about bioinformatics >Means... >What is the base of bioinformatics >What it includes >How it helpful to us > >Please send me information at princess01232001 at rediffmail.com > >Thanks u very much in advance > > > > > > From obj at obj.hopto.org Sat Jan 17 10:25:31 2004 From: obj at obj.hopto.org (Andrius) Date: Sat, 17 Jan 2004 17:25:31 +0200 Subject: [BiO BB] about bioinformatics In-Reply-To: <20040117085211.3371.qmail@webmail6.rediffmail.com> References: <20040117085211.3371.qmail@webmail6.rediffmail.com> Message-ID: <400953EB.8010902@obj.hopto.org> anyway you can look at http://www.ebi.ac.uk/2can/. this is a good site and they do provide the answer in a form of a novell..more or less:). Dhruti B Pathak wrote: >hi friends > >I want some information about bioinformatics >Means... >What is the base of bioinformatics >What it includes >How it helpful to us > >Please send me information at princess01232001 at rediffmail.com > >Thanks u very much in advance > > > > > > From B.A.T.Svensson at lumc.nl Sat Jan 17 08:38:59 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Sat, 17 Jan 2004 14:38:59 +0100 Subject: [BiO BB] about bioinformatics Message-ID: I had a fast glare at the site, and it is seams to be kind of comprehensive. However the problem is that the answer seams to varies depending on who you ask. ;) //Anders -----Original Message----- From: Andrius To: bio_bulletin_board at bioinformatics.org Sent: 2004-01-17 16:25 Subject: Re: [BiO BB] about bioinformatics anyway you can look at http://www.ebi.ac.uk/2can/. this is a good site and they do provide the answer in a form of a novell..more or less:). Dhruti B Pathak wrote: >hi friends > >I want some information about bioinformatics >Means... >What is the base of bioinformatics >What it includes >How it helpful to us > >Please send me information at princess01232001 at rediffmail.com > >Thanks u very much in advance > > > > > > _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Sat Jan 17 09:27:14 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 17 Jan 2004 14:27:14 -0000 (GMT) Subject: [BiO BB] about bioinformatics In-Reply-To: <20040117085211.3371.qmail@webmail6.rediffmail.com> References: <20040117085211.3371.qmail@webmail6.rediffmail.com> Message-ID: <34739.213.107.104.171.1074349634.squirrel@www.mrc-dunn.cam.ac.uk> here is an imaginative description... http://bio.cc/Bioinformatics/definition_of_bioinformatics.html ++ Dhruti B Pathak-- > > hi friends > > I want some information about bioinformatics > Means... > What is the base of bioinformatics > What it includes > How it helpful to us > > Please send me information at princess01232001 at rediffmail.com > > Thanks u very much in advance From gary at www.bioinformatics.org Sat Jan 17 11:06:16 2004 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Sat, 17 Jan 2004 11:06:16 -0500 (EST) Subject: [BiO BB] basic bioinformatics In-Reply-To: <20040117082754.31623.qmail@webmail30.rediffmail.com> Message-ID: Hi Dhruti, Check out : http://bioinformatics.org/faq Regards, g. On 17 Jan 2004, Dhruti B Pathak wrote: > hi everybody, What is bioinformatics What is the basic thing of bioinformatics How it helps in regular life What is its use thanks From shenhav at wicc.weizmann.ac.il Thu Jan 15 11:35:30 2004 From: shenhav at wicc.weizmann.ac.il (Barak Shenhav) Date: Thu, 15 Jan 2004 18:35:30 +0200 Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? Message-ID: <3FF951C8@wiccweb> >===== Original Message From bio_bulletin_board at bioinformatics.org ===== Snip 8< ... >> Am I wrong? > >No you are not wrong, but perhaps we are just privilaged? >Anyone want to borrow my idle time? Snip 8< I am starving for CPU! ==================================== Barak Shenhav Department of Molecular Genetics Weizmann Institute of Science +972 8 9343098 (office) +972 8 9344487 (fax) +972 5 2955550 (cellular) From valery at biozak.com Thu Jan 15 19:33:01 2004 From: valery at biozak.com (Valery Miftakhov) Date: Thu, 15 Jan 2004 16:33:01 -0800 Subject: [BiO BB] Accelerating HMM in FPGA Message-ID: <4007313D.6020102@biozak.com> Hi All, I have just stumbled across this older post from one of the members of this group, Venu Kobe, and I am interested in the progress that you, Venu, and possibly anyone else had in accelerating HMM in FPGA. Please let me know. -- Valery Miftakhov, Ph.D. -- (650)-906-0477 ---------------- Hello everyone, I am graduate student in computer engineering doing my thesis in the following topic: "Matching Protein sequences with HMM models in FPGAs ( Field Programmable Gate Arrays ) using Run Time Reconfiguration" If you are familiar with Decypher tool from TimeLogic, my work involves something similar to that. Decypher is a very comprehensive and expensive tool and sure it does deliver excellent performance compared to the software tools such as HMMR, SAM or the other tools. My work falls in between the software solution and that of Decypher. Specifically, when developed my tool would be considerably faster than that of the software tools currently available and also be affordable at a fraction of the cost of using Decypher. I have just started digging into Bioinformatics and have read quite a number of papers and all, but I am still a little confused and would like any comments or suggestions from you: 1) Does my tool make any sense at all? 2) What is the current customer base like for this technology? 3) What sort of companies do the work of matching protein/DNA sequences with existing models? 4) Is there a need for a less comprehensive and less expensive tool as opposed to Decypher for customers who want to get it done a lot less cheaper but wouldnt mind the extra penalty in performace ( ofcourse will be very much better than that of the software searching) 5) Any comments, questions, suggestions? 6) Any pointers for me in terms of websites or resources. I would very much appreciate your comments TIA Kode From cdwan at mail.ahc.umn.edu Sun Jan 18 16:05:12 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Sun, 18 Jan 2004 15:05:12 -0600 (CST) Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <3FF951C8@wiccweb> References: <3FF951C8@wiccweb> Message-ID: > I am starving for CPU! Would it be sufficient to provide a set of interfaces (web services, RMI's, whatever is hip these days) to fairly standard analysis tools, or do you need to run custom executables? Using existing technology, it's tricky but very achievable to share our spare cycles for known analyses with collaborators. So long as we're able to speak the language of "BLASTN this query vs NCBI dbEST no older than January 1, 2004", we can provide a moderate amount of CPU to a lot of people at minimal effort. Would that be useful? More concretely, who else would be willing to share their cycles, and who would be willing to make use of such a service? The harder problem ("~/a.out -i /data/freakishly_huge.dat > 10.1.1.1:/export/foo.out") involves solving quite a few problems: data movement, binary incompatibility, privacy, and trust to name just a few. Of these, trust is by far the largest. Users need to trust that their results are accurate, and providers need to trust that users are well behaved. Or perhaps I'm just very confused about the real problems out there in the world. -Chris Dwan The University of Minnesota From DNGARB at telefonica.net Mon Jan 19 06:12:04 2004 From: DNGARB at telefonica.net (DNGARB at telefonica.net) Date: Mon, 19 Jan 2004 12:12:04 +0100 Subject: [BiO BB] struture viewing Message-ID: <1dbd941dec6e.1dec6e1dbd94@teleline.es> Hello, another program for use at Linux is DINO (http://www.dino3d.org/). It is incredible and very professional. Its only problem is the command language... perhaps a little strange. Have a look to the tutorial: is very helpful. davidjm ----- Mensaje Original ----- De: Joe Landman Fecha: Viernes, Enero 16, 2004 6:55 am Asunto: Re: [BiO BB] struture viewing > I have been quite happy with VMD (http://www.ks.uiuc.edu), > Ghemical, > Pymol, and a few others. If you are an old XMol user, JMol will > feel > very familiar. There are quite a few others as well. > > Joe > > Iddo Friedberg wrote: > > > Hi Pankaj, > > > > I have always been partial to PyMol for visualization and > terrific > > graphics. Swiss-PDB viewer is good on visualizatoin (not as > great as > > PyMol), but adds modelling functionality, should you require it. > > > > People I know praise Molscipt for pulish-quality graphics. But I > am > > not experienced with that. > > > > Hope this helps, > > > > Iddo > > > > > > Pankaj wrote: > > > >> hello everyone, > >> i have been using insightII (on SGI) for protein structure > viewing and > >> modelling of proteins and it seemed very friendly. now i have > shifted>> to a linux machine on which insightII does not work. i > have lot of > >> options for macromolecular viewing tools (eg rasmol, vmd etc) for > >> linux but i cannot decide which is the best. i tried rasmol but > it was > >> not very competent in terms that it didnt have many options. can > >> someone help in this regard. > >> thanks in advance > >> pankaj > >> > > > > -- > Joseph Landman, Ph.D > Scalable Informatics LLC, > email: landman at scalableinformatics.com > web : http://scalableinformatics.com > phone: +1 734 612 4615 > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From 1203ab003 at cdl.msitprogram.net Mon Jan 19 10:20:18 2004 From: 1203ab003 at cdl.msitprogram.net (Krishna Chaitanya Atkuru) Date: Mon, 19 Jan 2004 20:50:18 +0530 (IST) Subject: [BiO BB] Genome Database schemas Message-ID: <2946.172.16.8.53.1074525618.squirrel@cdl.msitprogram.net> hi all, could some one help me out with the schemas of various databases? i have personally reffered the GDB but found that it was too huge.. for present(as iam novoice in this field) , i would be very happy to kick off with some databases(specialized databases) that are rather easy to understand( say arrayexpress GeneExpressionOmnibus,stanford microarray database) as well as easy to implement... thanking you krishna chaitanya atkuru krishnachaitanya_iiit at msitprogram.net -- krishna chaitanya krishnachaitanya_iiit at msitprogram.net From lry_biocomp at hotmail.com Mon Jan 19 16:47:32 2004 From: lry_biocomp at hotmail.com (Renyi Liu) Date: Mon, 19 Jan 2004 16:47:32 -0500 Subject: [BiO BB] Please Help: d2_cluster output format Message-ID: Hi, All, Can anybody tell me the format of d2_cluster output format? The output has several columns of numbers, but I do not know the meaning of each. I tried to find the documentation on the web, but was not successfull. Any help will be highly appreciated. Thanks, Renyi _________________________________________________________________ Check out the coupons and bargains on MSN Offers! http://shopping.msn.com/softcontent/softcontent.aspx?scmId=1418 From CMoussalli03 at msn.com Mon Jan 19 15:03:25 2004 From: CMoussalli03 at msn.com (CAROLE S MOUSSALLI) Date: Mon, 19 Jan 2004 15:03:25 -0500 Subject: [BiO BB] Interview request for biotech book Message-ID: Greetings to all super-busy, much-in-demand bioinformatics professionals: I am a recent graduate of Columbia Business School and have been commissioned by Vault, Inc. to write a career development guide on the Biotech industry for early to mid-career professionals. I need help identifying someone who is willing to speak with me for approx. 45 minutes for a Day-in-the-Life interview. Questions and format is set; full confidentiality is assured. Samples of similar profiles are available. The best candidate will have been on the job for 1-3 years and have graduated with a degree in bioinformatics. On behalf of my publisher, I would like to thank everyone who can give me some time and attention. Kind Regards, Carole Carole S. Moussalli cmoussalli03 at gsb.columbia.edu 23 Maplewood Street Watertown, MA 02472-3501 Tel: 617-926-6782 Fax: 617-926-6783 Cell: 917-667-6186 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: color_stripe.gif Type: image/gif Size: 3753 bytes Desc: not available URL: From pankaj at nii.res.in Wed Jan 21 03:55:56 2004 From: pankaj at nii.res.in (Pankaj) Date: Wed, 21 Jan 2004 14:25:56 +0530 (IST) Subject: [BiO BB] alignment problem Message-ID: hi all, i have 100 sequences. i want to find the percentage simialrity of every sequence to every other sequence. ie i want to prepare a 100X100 matrix. i m using local blast from ncbi to find the similarity. but sometimes the output file from blast has 2 alignments between the sequences. ie sequence1 with sequence2 has 2 possible alignments (ie over different parts of the sequences). how do i find the percentage similarity between the sequences. if i multipli align these 100 sequences by clustalw, i can see large gaps in certain regions but i know that all these sequences catalyse the same reaction. thanks in advance pankaj From lry_biocomp at hotmail.com Wed Jan 21 11:21:33 2004 From: lry_biocomp at hotmail.com (Renyi Liu) Date: Wed, 21 Jan 2004 11:21:33 -0500 Subject: [BiO BB] alignment problem Message-ID: Hi, Pankaj, Since the number of sequences is not so big, I would use Smith-Waterman algorithm to obtain optimal local alignment between any two sequences. For multiple alignment, I would try T_Coffee or/and Dialign2. Both program can be downloaded from the internet, but I am not sure if they can handle 100 sequences. Good luck, Renyi >From: Pankaj >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] alignment problem >Date: Wed, 21 Jan 2004 14:25:56 +0530 (IST) > >hi all, >i have 100 sequences. i want to find the percentage simialrity of >every sequence to every other sequence. ie i want to prepare a 100X100 >matrix. i m using local blast from ncbi to find the similarity. but >sometimes the output file from blast has 2 alignments between the >sequences. ie sequence1 with sequence2 has 2 possible alignments (ie >over different parts of the sequences). how do i find the percentage >similarity between the sequences. >if i multipli align these 100 sequences by clustalw, i can see large >gaps in certain regions but i know that all these sequences catalyse >the same reaction. >thanks in advance >pankaj > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Get a FREE online virus check for your PC here, from McAfee. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 From sharmash at pn2.vsnl.net.in Wed Jan 21 12:03:12 2004 From: sharmash at pn2.vsnl.net.in (SH Sharma) Date: Wed, 21 Jan 2004 22:33:12 +0530 Subject: [BiO BB] 3d modeling Message-ID: <000801c3e040$754cc4c0$115941db@sharmash> We are a group (5) computer engineering students. developing a biosuite comprising of sevaral bioinformatic tools. (1) we need the basics of 3D modeling in bioinformatics. (2) are there any algorithms to model proteins. If yes which are they> how to know about these (3) are there any software used for modeling and simulation. -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.A.T.Svensson at lumc.nl Thu Jan 22 02:08:50 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Thu, 22 Jan 2004 08:08:50 +0100 Subject: [BiO BB] 3d modeling Message-ID: 1. http://www.google.com/search?q=3D+modeling+in+bioinformatics&ie=UTF-8&oe=UTF -8&hl=nl&btnG=Google+zoeken&lr= 2. http://www.google.com/search?hl=nl&ie=UTF-8&oe=UTF-8&q=algorithms+to+model+p roteins&btnG=Google+zoeken&lr= 3. See above. -----Original Message----- From: SH Sharma To: bio_bulletin_board at bioinformatics.org Sent: 2004-01-21 18:03 Subject: [BiO BB] 3d modeling We are a group (5) computer engineering students. developing a biosuite comprising of sevaral bioinformatic tools. (1) we need the basics of 3D modeling in bioinformatics. (2) are there any algorithms to model proteins. If yes which are they> how to know about these (3) are there any software used for modeling and simulation. From dmb at mrc-dunn.cam.ac.uk Thu Jan 22 04:06:49 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 22 Jan 2004 09:06:49 -0000 (GMT) Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <3FF951C8@wiccweb> References: <3FF951C8@wiccweb> Message-ID: <44428.193.60.81.207.1074762409.squirrel@www.mrc-dunn.cam.ac.uk> ++ Barak Shenhav-- >>===== Original Message From bio_bulletin_board at bioinformatics.org ===== > > Snip 8< ... > >>> Am I wrong? >> >>No you are not wrong, but perhaps we are just privilaged? >>Anyone want to borrow my idle time? > > Snip 8< > > I am starving for CPU! What are you doing? > ==================================== > Barak Shenhav > Department of Molecular Genetics > Weizmann Institute of Science > +972 8 9343098 (office) > +972 8 9344487 (fax) > +972 5 2955550 (cellular) > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From shenhav at wicc.weizmann.ac.il Thu Jan 22 07:18:24 2004 From: shenhav at wicc.weizmann.ac.il (Barak Shenhav) Date: Thu, 22 Jan 2004 14:18:24 +0200 Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? Message-ID: <400EF739@wiccweb> >> Snip 8< ... >> >>> Am I wrong? >>> >>>No you are not wrong, but perhaps we are just privilaged? >>>Anyone want to borrow my idle time? >> >> Snip 8< >> >> I am starving for CPU! > >What are you doing? > Computer simulations of early evolution. See: http://ool.weizmann.ac.il ==================================== Barak Shenhav Department of Molecular Genetics Weizmann Institute of Science +972 8 9343098 (office) +972 8 9344487 (fax) +972 5 2955550 (cellular) From madhavi+blc at cs.cmu.edu Thu Jan 22 18:04:37 2004 From: madhavi+blc at cs.cmu.edu (Madhavi Ganapathiraju) Date: Thu, 22 Jan 2004 18:04:37 -0500 Subject: [BiO BB] BLC2004: Biological Language Conference In-Reply-To: <5.2.0.9.2.20031003162439.020a0e28@128.2.254.145> Message-ID: <5.2.0.9.1.20040111195105.02896a38@ux15.sp.cs.cmu.edu> BLC2004: 2nd Biological Language Conference, Carnegie Mellon University, Pittsburgh, USA http://flan.blm.cs.cmu.edu/blc2004/ Scope: Integration of language technologies in bioinformatics/computational biology research Protein sequences from different organisms may be viewed as texts written in different languages. The mapping of protein sequence to their structure, dynamics and function then becomes analogous to the mapping of words to meaning in natural languages. This analogy can be exploited by application of statistical language modeling and text classification techniques to biological sequences, thereby generating testable hypotheses regarding the fundamental building blocks of "protein sequence language". The biology-language analogy enables novel applications of language technologies to the biology domain, but is to a great extent overlapping with existing other computational biology/bioinformatics applications. The purpose of the Biological Language Conference is to facilitate scientific exchange between researchers using the language analogy approach directly and researchers using other approaches. We invite papers in the following areas of interest secondary structure prediction tertiary structure prediction repetitive fold/supersecondary structure prediction membrane protein-specific prediction challenges protein folding/misfolding protein dynamics and conformational changes protein-protein interactions protein/gene networks and pathways microarray analysis protein function prediction DNA sequence analysis efficient sequence processing genome evolution/comparison sequence alignment protein family classification immune system database/toolkit development mass spectrometry data analysis Key Dates ======= June 1st, 2004 Deadline for electronic paper submission August 1st, 2004 Notification of acceptance August 15th, 2004 Final camera-ready manuscript due October 15th, 2004 Registration deadline November 18-19, 2004 Conference Conference is organized by the NSF funded Centre for Biological Language Modeling (http://www.cs.cmu.edu/~blmt) Contact: Judith Klein-Seetharaman judithks at cs.cmu.edu BLC2003: http://flan.blm.cs.cmu.edu/meeting2003/ From prathibha_562 at yahoo.co.in Fri Jan 23 01:43:26 2004 From: prathibha_562 at yahoo.co.in (=?iso-8859-1?q?prathibha=20bharathi?=) Date: Fri, 23 Jan 2004 06:43:26 +0000 (GMT) Subject: [BiO BB] alignment problem In-Reply-To: Message-ID: <20040123064326.72122.qmail@web8206.mail.in.yahoo.com> sir...plz tell me how to perform statistical evaluation of seq alignment and calculate Z-score am a comp science student from india thank you sir, from prathibha bharathi Renyi Liu wrote: Hi, Pankaj, Since the number of sequences is not so big, I would use Smith-Waterman algorithm to obtain optimal local alignment between any two sequences. For multiple alignment, I would try T_Coffee or/and Dialign2. Both program can be downloaded from the internet, but I am not sure if they can handle 100 sequences. Good luck, Renyi >From: Pankaj >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] alignment problem >Date: Wed, 21 Jan 2004 14:25:56 +0530 (IST) > >hi all, >i have 100 sequences. i want to find the percentage simialrity of >every sequence to every other sequence. ie i want to prepare a 100X100 >matrix. i m using local blast from ncbi to find the similarity. but >sometimes the output file from blast has 2 alignments between the >sequences. ie sequence1 with sequence2 has 2 possible alignments (ie >over different parts of the sequences). how do i find the percentage >similarity between the sequences. >if i multipli align these 100 sequences by clustalw, i can see large >gaps in certain regions but i know that all these sequences catalyse >the same reaction. >thanks in advance >pankaj > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Get a FREE online virus check for your PC here, from McAfee. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Yahoo! India Mobile: Ringtones, Wallpapers, Picture Messages and more.Download now. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Fri Jan 23 04:58:28 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 23 Jan 2004 09:58:28 -0000 (GMT) Subject: [BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics? In-Reply-To: <400EF739@wiccweb> References: <400EF739@wiccweb> Message-ID: <33461.213.107.104.171.1074851908.squirrel@www.mrc-dunn.cam.ac.uk> ++ Barak Shenhav-- >>> Snip 8< ... >>> >>>> Am I wrong? >>>> >>>>No you are not wrong, but perhaps we are just privilaged? >>>>Anyone want to borrow my idle time? >>> >>> Snip 8< >>> >>> I am starving for CPU! >> >>What are you doing? >> > Computer simulations of early evolution. See: > > http://ool.weizmann.ac.il Great! Did you talk at the EMBL student symposium a while back? > ==================================== > Barak Shenhav > Department of Molecular Genetics > Weizmann Institute of Science > +972 8 9343098 (office) > +972 8 9344487 (fax) > +972 5 2955550 (cellular) > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Fri Jan 23 05:58:23 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 23 Jan 2004 10:58:23 -0000 (GMT) Subject: [BiO BB] alignment problem In-Reply-To: <20040123064326.72122.qmail@web8206.mail.in.yahoo.com> References: <20040123064326.72122.qmail@web8206.mail.in.yahoo.com> Message-ID: <34236.213.107.104.171.1074855503.squirrel@www.mrc-dunn.cam.ac.uk> > Since the number of sequences is not so big, I would use Smith-Waterman algorithm > to obtain optimal local alignment between any two sequences. Is making a multiple alignment as simple as compiling all pairwise alignments to a reference sequence? How do you evaluate the performance of this to a 'true' multiple alignment? From stuartcraigie at hotmail.com Fri Jan 23 06:47:44 2004 From: stuartcraigie at hotmail.com (stuart craigie) Date: Fri, 23 Jan 2004 11:47:44 +0000 Subject: [BiO BB] Nautilus LIMS for microarray work Message-ID: Dear all, Has anyone used Thermo's Nautilus LIMS for handling microarray experiments? I'm looking at configuring Nautilus so that we can track the production and use of spotted cDNA microarrays. I'm at the early planning stages so any advice on planning, designing and implementing such a system would be much appreciated. Regards, Stuart Craigie. SEB Department Veterinary Laboratories Agency Woodham Lane New Haw Addlestone Surrey KT15 3NB tel: 01932 357860 _________________________________________________________________ Express yourself with cool new emoticons http://www.msn.co.uk/specials/myemo From landman at scalableinformatics.com Mon Jan 26 00:55:30 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 26 Jan 2004 00:55:30 -0500 Subject: [BiO BB] mpiBLAST 1.2.0 RPM's available Message-ID: <1075096529.4484.544.camel@protein.scalableinformatics.com> Hi Folks: We built some source and binary RPM's for mpiBLAST 1.2.0. You can find them at http://downloads.scalableinformatics.com/downloads/mpiblast/ or linked off of our main page http://scalableinformatics.com . These RPM's assume you have an operational and functional mpich installation. They should work with most architectures, though I am working on fixing the Opteron build. We created these as people seemed to have some trouble building the package, and installing it on their systems. If you grab the binary version, please edit the /usr/local/etc/mpiblast.conf file as per the instructions on the mpiBLAST page at http://mpiblast.lanl.gov . Please send us a note on any problems you encounter with this packaging. To install the binary version, download the appropriate binary and as root, run rpm -Uvh mpiBLAST-1.2.0-3.i686.rpm This assumes you have grabbed the i686 architecture binary. If you would prefer to build from source, make sure you have a functional mpich install with mpe, have it in your path and be able to compile with mpiCC, and then run: rpmbuild --rebuild mpiBLAST-1.2.0-3.src.rpm to build a binary. Then use the resulting binary RPM to install. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From prandeep7 at hotmail.com Mon Jan 26 06:15:55 2004 From: prandeep7 at hotmail.com (prandeep borah) Date: Mon, 26 Jan 2004 16:45:55 +0530 Subject: [BiO BB] MS.c in Bioinformatics in distance education mood in india. Message-ID: hi, I have done my B.Sc in Bio-Chemistry(Botany) & also doning a Advance Diploma Course in Computer application. I m intersted in doing M.Sc/advance diploma in Bioinformatics. I want to know abt the institute who gives such course through Distance learning mood in India . Thanking u . prandeep borah tezpur(Assam) _________________________________________________________________ Marriage? Join BharatMatrimony.com for free. http://www.bharatmatrimony.com/cgi-bin/bmclicks1.cgi?74 From cromologic at yahoo.com Wed Jan 28 04:59:19 2004 From: cromologic at yahoo.com (BORN II CODE) Date: Wed, 28 Jan 2004 01:59:19 -0800 (PST) Subject: [BiO BB] Please guide me Message-ID: <20040128095919.48669.qmail@web12823.mail.yahoo.com> Hi ! i am a still new to bioinformatics.currently i am working on developing a database with the intergration of xml.as far as i understand, most of the databanks has its own data(heterogenous format).what are the fields that i must know in order to develop a database?how can i retrieve biological data from these databanks.i only know things at the surface level.many of the articles are very confusing.as far as i am concern there are things like protein sequence and DNA sequence.where can i get a sample database table containing field for such entity?? my plan of architecture (architecture for the system which i am going to develop) consist of a database which will be built using Oracle 9i, XML and SAX parser for converting various formats into a unified format plus PERL for communicating with the bio databank's servers. please advise if this is feasible or redundant otherwise.i am pretty much perplexed in determing the right data types for my database.please guide me and i am not asking anyone of you to develop the systems for me.i am willing to learn and develop concurrently with advice from you. please help me. sargunan --------------------------------- Do you Yahoo!? Yahoo! SiteBuilder - Free web site building tool. Try it! -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joel.Dudley at asu.edu Wed Jan 28 12:02:53 2004 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Wed, 28 Jan 2004 10:02:53 -0700 Subject: [BiO BB] Position Available: Bioinformatics Software Developer Message-ID: <9EAE2E44897BC749ACB3A62683B2C8D123F07A@ex4.asurite.ad.asu.edu> The Center for Functionaly Evolutionary Genomics at the Arizona BioDesign Institute is currently seeking software developers. Please refer to the official Human Resources posting for details (Note: the HR assigned position title is a misnomer): http://www.hr.asu.edu/vacancy_notice/vacancy_posting.asp?id=113788 Joel Dudley Faculty Research Associate Center for Evolutionary Functional Genomics Arizona Biodesign Institute @ Arizona State University P.S.: If open position postings such as this are not allowed by the etiquette of this list please inform me so that I do not make the same mistake in the future. This posting was sent to this list for the benefit of qualified list members that are currently seeking employment. From B.A.T.Svensson at lumc.nl Thu Jan 29 07:36:19 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Thu, 29 Jan 2004 13:36:19 +0100 Subject: [BiO BB] Please guide me Message-ID: I would suggest study some relational database theory first. The the rest will solve it self afterwards. -----Original Message----- From: BORN II CODE To: bio_bulletin_board at bioinformatics.org Sent: 2004-01-28 10:59 Subject: [BiO BB] Please guide me Hi ! i am a still new to bioinformatics.currently i am working on developing a database with the intergration of xml.as far as i understand, most of the databanks has its own data(heterogenous format).what are the fields that i must know in order to develop a database?how can i retrieve biological data from these databanks.i only know things at the surface level.many of the articles are very confusing.as far as i am concern there are things like protein sequence and DNA sequence.where can i get a sample database table containing field for such entity?? my plan of architecture (architecture for the system which i am going to develop) consist of a database which will be built using Oracle 9i, XML and SAX parser for converting various formats into a unified format plus PERL for communicating with the bio databank's servers. please advise if this is feasible or redundant otherwise.i am pretty much perplexed in determing the right data types for my database.please guide me and i am not asking anyone of you to develop the systems for me.i am willing to learn and develop concurrently with advice from you. please help me. sargunan From jrs at denny.farviolet.com Thu Jan 29 17:13:12 2004 From: jrs at denny.farviolet.com (Jeremy Semeiks) Date: Thu, 29 Jan 2004 14:13:12 -0800 Subject: [BiO BB] Please guide me In-Reply-To: <20040128095919.48669.qmail@web12823.mail.yahoo.com> References: <20040128095919.48669.qmail@web12823.mail.yahoo.com> Message-ID: <20040129221312.GY5600@64.81.242.180> On Wed, Jan 28, 2004 at 01:59:19AM -0800, BORN II CODE wrote: > Hi ! i am a still new to bioinformatics.currently i am working on > developing a database with the intergration of xml.as far as i > understand, most of the databanks has its own data(heterogenous > format).what are the fields that i must know in order to develop a > database?how can i retrieve biological data from these databanks.i > only know things at the surface level.many of the articles are very > confusing.as far as i am concern there are things like protein > sequence and DNA sequence.where can i get a sample database table > containing field for such entity?? There are a few unified biological schemas out there: BioSQL, Chado, GUS, and Ensembl. You might be able to adapt one of these pre-made schemas; the relevant factors are what biological data you need to store, exactly, and what you're interested in doing with them. At the moment, I don't think there's any single comprehensive solution. You can use Bioperl to parse most of the standard flat-text databanks. Good luck, Jeremy From obj at obj.hopto.org Thu Jan 29 19:56:00 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 02:56:00 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <20040129221312.GY5600@64.81.242.180> References: <20040128095919.48669.qmail@web12823.mail.yahoo.com> <20040129221312.GY5600@64.81.242.180> Message-ID: <4019ABA0.2050407@obj.hopto.org> Jeremy Semeiks wrote: >On Wed, Jan 28, 2004 at 01:59:19AM -0800, BORN II CODE wrote: > > > >>Hi ! i am a still new to bioinformatics.currently i am working on >>developing a database with the intergration of xml.as far as i >>understand, most of the databanks has its own data(heterogenous >>format).what are the fields that i must know in order to develop a >>database?how can i retrieve biological data from these databanks.i >>only know things at the surface level.many of the articles are very >>confusing.as far as i am concern there are things like protein >>sequence and DNA sequence.where can i get a sample database table >>containing field for such entity?? >> >> > >There are a few unified biological schemas out there: BioSQL, Chado, >GUS, and Ensembl. You might be able to adapt one of these pre-made >schemas; the relevant factors are what biological data you need to >store, exactly, and what you're interested in doing with them. At the >moment, I don't think there's any single comprehensive solution. > > Won't it be a good idea to develop one. It seems that tools for doing bioinformatics are still maturing and one of the things to make them mature are common schemas and standards. I think there's a nice potential for developers in this direction. >You can use Bioperl to parse most of the standard flat-text databanks. > >Good luck, >Jeremy >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From B.A.T.Svensson at lumc.nl Thu Jan 29 18:36:03 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 30 Jan 2004 00:36:03 +0100 Subject: [BiO BB] Please guide me Message-ID: What would the benefits of a common schema be? -----Original Message----- From: Andrius Won't it be a good idea to develop one. It seems that tools for doing bioinformatics are still maturing and one of the things to make them mature are common schemas and standards. I think there's a nice potential for developers in this direction. From dmb at mrc-dunn.cam.ac.uk Thu Jan 29 18:31:25 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 29 Jan 2004 23:31:25 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: <4019ABA0.2050407@obj.hopto.org> References: <20040128095919.48669.qmail@web12823.mail.yahoo.com> <20040129221312.GY5600@64.81.242.180> <4019ABA0.2050407@obj.hopto.org> Message-ID: <35050.213.107.104.171.1075419085.squirrel@www.mrc-dunn.cam.ac.uk> ++ Andrius-- > Jeremy Semeiks wrote: > >>On Wed, Jan 28, 2004 at 01:59:19AM -0800, BORN II CODE wrote: >> >> >> >>>Hi ! i am a still new to bioinformatics.currently i am working on developing a >>> database with the intergration of xml.as far as i >>>understand, most of the databanks has its own data(heterogenous >>>format).what are the fields that i must know in order to develop a database?how >>> can i retrieve biological data from these databanks.i only know things at the >>> surface level.many of the articles are very confusing.as far as i am concern >>> there are things like protein >>>sequence and DNA sequence.where can i get a sample database table containing >>> field for such entity?? >>> >>> >> >>There are a few unified biological schemas out there: BioSQL, Chado, GUS, and >> Ensembl. You might be able to adapt one of these pre-made schemas; the relevant >> factors are what biological data you need to store, exactly, and what you're >> interested in doing with them. At the moment, I don't think there's any single >> comprehensive solution. >> >> > Won't it be a good idea to develop one. It seems that tools for doing > bioinformatics are still maturing and > one of the things to make them mature are common schemas and standards. I think > there's a nice potential > for developers in this direction. me too >>You can use Bioperl to parse most of the standard flat-text databanks. >> >>Good luck, >>Jeremy >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Thu Jan 29 18:33:34 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 29 Jan 2004 23:33:34 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: References: Message-ID: <35087.213.107.104.171.1075419214.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- > What would the benefits of a common schema be? interoperability, foundation of the field, common development environment, growth I guess people can add more. > -----Original Message----- > From: Andrius > > Won't it be a good idea to develop one. It seems that tools for doing > bioinformatics are still maturing and one of the things to make them mature are > common schemas and standards. > > I think there's a nice potential for developers in this direction. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From gary at www.bioinformatics.org Thu Jan 29 19:05:16 2004 From: gary at www.bioinformatics.org (Gary Van Domselaar) Date: Thu, 29 Jan 2004 19:05:16 -0500 (EST) Subject: [BiO BB] Please guide me In-Reply-To: <35087.213.107.104.171.1075419214.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: Hi guys, I think a common api to biological data is more important than a common schema. People like to customize their schemas according to a variety of things like speed, normalization, denormalization. Check out the biomoby project: http://www.biomoby.org Regards, g. On Thu, 29 Jan 2004, Dan Bolser wrote: > ++ HKG-- > > What would the benefits of a common schema be? > > interoperability, foundation of the field, common development environment, growth > > I guess people can add more. > > > -----Original Message----- > > From: Andrius > > > > Won't it be a good idea to develop one. It seems that tools for doing > > bioinformatics are still maturing and one of the things to make them mature are > > common schemas and standards. > > > > I think there's a nice potential for developers in this direction. > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From B.A.T.Svensson at lumc.nl Fri Jan 30 02:32:19 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 30 Jan 2004 08:32:19 +0100 Subject: [BiO BB] Please guide me Message-ID: >> What would the benefits of a common schema be? >interoperability, foundation of the field, common development >environment, growth A common schem wont help one to achive that. >I guess people can add more. From Austin.Tanney at arragen.com Fri Jan 30 04:01:32 2004 From: Austin.Tanney at arragen.com (Austin Tanney) Date: Fri, 30 Jan 2004 09:01:32 -0000 Subject: [BiO BB] Please guide me Message-ID: Use of common schema is a huge advantage to biological research in general. I work in the microarray field and a great deal of work is ongoing into the process of standardisation of data and storage formats. The MGED have developed their own mark-up language (MAGE-ML) as well as the MIAME standards. This, combined with the development of the EBI's arayexpress database, will be greatly facilitative to the sharing of microarray data between researchers. Common schema's in general have wide applications both for industry, in that it allows multi site organisations to easily share data, and for academia where the transfer of information between research groups can be essential. Austin Dr. Austin Tanney Senior Scientist Arragen Ltd. E-mail: Austin.Tanney at Arragen.com Phone: +44 283839 5750 Fax: +44 283839 8676 Mobile: +44 7968 013939 -----Original Message----- From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] Sent: 29 January 2004 23:34 To: bio_bulletin_board at bioinformatics.org Cc: B.A.T.Svensson at lumc.nl Subject: RE: [BiO BB] Please guide me ++ HKG-- > What would the benefits of a common schema be? interoperability, foundation of the field, common development environment, growth I guess people can add more. > -----Original Message----- > From: Andrius > > Won't it be a good idea to develop one. It seems that tools for doing > bioinformatics are still maturing and one of the things to make them mature are > common schemas and standards. > > I think there's a nice potential for developers in this direction. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern Ireland From B.A.T.Svensson at lumc.nl Fri Jan 30 04:30:05 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 30 Jan 2004 10:30:05 +0100 Subject: [BiO BB] Please guide me Message-ID: And what precisely is the relation between a common XML file format and a "common" database schema? -----Original Message----- From: Austin Tanney To: bio_bulletin_board at bioinformatics.org Sent: 2004-01-30 10:01 Subject: RE: [BiO BB] Please guide me Use of common schema is a huge advantage to biological research in general. I work in the microarray field and a great deal of work is ongoing into the process of standardisation of data and storage formats. The MGED have developed their own mark-up language (MAGE-ML) as well as the MIAME standards. This, combined with the development of the EBI's arayexpress database, will be greatly facilitative to the sharing of microarray data between researchers. Common schema's in general have wide applications both for industry, in that it allows multi site organisations to easily share data, and for academia where the transfer of information between research groups can be essential. Austin Dr. Austin Tanney Senior Scientist Arragen Ltd. E-mail: Austin.Tanney at Arragen.com Phone: +44 283839 5750 Fax: +44 283839 8676 Mobile: +44 7968 013939 -----Original Message----- From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] Sent: 29 January 2004 23:34 To: bio_bulletin_board at bioinformatics.org Cc: B.A.T.Svensson at lumc.nl Subject: RE: [BiO BB] Please guide me ++ HKG-- > What would the benefits of a common schema be? interoperability, foundation of the field, common development environment, growth I guess people can add more. > -----Original Message----- > From: Andrius > > Won't it be a good idea to develop one. It seems that tools for doing > bioinformatics are still maturing and one of the things to make them mature are > common schemas and standards. > > I think there's a nice potential for developers in this direction. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern Ireland _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Fri Jan 30 04:18:38 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 30 Jan 2004 09:18:38 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: References: <35087.213.107.104.171.1075419214.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <46723.193.60.81.207.1075454318.squirrel@www.mrc-dunn.cam.ac.uk> ++ Gary Van Domselaar-- > > Hi guys, > > I think a common api to biological data is more important than a common schema. > People like to customize their schemas according to a variety of things like > speed, normalization, denormalization. This is true - I don't think a grand centralised schema would ever be possible or correct, but some how I think a core will emerge by somehow giving people a common exchange mechanism within the framework of a schema or datamodel. > Check out the biomoby project: > > http://www.biomoby.org Cheers for this, Dan. > Regards, > > g. > > > On Thu, 29 Jan 2004, Dan Bolser wrote: > >> ++ HKG-- >> > What would the benefits of a common schema be? >> >> interoperability, foundation of the field, common development environment, >> growth >> >> I guess people can add more. >> >> > -----Original Message----- >> > From: Andrius >> > >> > Won't it be a good idea to develop one. It seems that tools for doing >> bioinformatics are still maturing and one of the things to make them mature >> are common schemas and standards. >> > >> > I think there's a nice potential for developers in this direction. >> > >> > _______________________________________________ >> > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> From Austin.Tanney at arragen.com Fri Jan 30 04:54:49 2004 From: Austin.Tanney at arragen.com (Austin Tanney) Date: Fri, 30 Jan 2004 09:54:49 -0000 Subject: [SPAM] - RE: [BiO BB] Please guide me - Found word(s) check out in the Text body. Message-ID: Yes, very true. I was coming more from the perspective that the more we attempt to standardise information management and exchange, the more likely we are to succeed. -----Original Message----- From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] Sent: 30 January 2004 09:19 To: gary at www.bioinformatics.org Cc: bio_bulletin_board at bioinformatics.org; B.A.T.Svensson at lumc.nl Subject: [SPAM] - RE: [BiO BB] Please guide me - Found word(s) check out in the Text body. ++ Gary Van Domselaar-- > > Hi guys, > > I think a common api to biological data is more important than a common schema. > People like to customize their schemas according to a variety of things like > speed, normalization, denormalization. This is true - I don't think a grand centralised schema would ever be possible or correct, but some how I think a core will emerge by somehow giving people a common exchange mechanism within the framework of a schema or datamodel. > Check out the biomoby project: > > http://www.biomoby.org Cheers for this, Dan. > Regards, > > g. > > > On Thu, 29 Jan 2004, Dan Bolser wrote: > >> ++ HKG-- >> > What would the benefits of a common schema be? >> >> interoperability, foundation of the field, common development environment, >> growth >> >> I guess people can add more. >> >> > -----Original Message----- >> > From: Andrius >> > >> > Won't it be a good idea to develop one. It seems that tools for doing >> bioinformatics are still maturing and one of the things to make them mature >> are common schemas and standards. >> > >> > I think there's a nice potential for developers in this direction. >> > >> > _______________________________________________ >> > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern Ireland From dmb at mrc-dunn.cam.ac.uk Fri Jan 30 04:34:46 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 30 Jan 2004 09:34:46 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: References: Message-ID: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- >>> What would the benefits of a common schema be? > >>interoperability, foundation of the field, common development >>environment, growth > > A common schem wont help one to achive that. Not directly no - but it would be a big help! Maybe this is a big prejudice of mine, but I am actually quite passionate about this idea. After all, when one mathematician talks to another, they have a common formal language with which to do so - chemists too and the same with comp-sci. Now, while every biologist damn well knows he has a common language to communicate with his peers, this language is not easily formalized. The previous examples are able to work by defining primitives and association rules, but in biology the primitives are already high level concepts, and the association rules are often the results of ongoing research activities. Thus these 'fundamentals' are not easy to agree - this is why we must develop a formal framework within which precise definitions and relationships can emerge pragmatically, in effect leading to a global schema. From the viewpoint of the philosophy of science I think this is how it works in the brains of biologists (I could be wrong), the difficulty is getting something similar to happen in a computer friendly way. I am 100% confident (maybe you see my prejudice) that this will happen someday. Ta, Dan. >>I guess people can add more. > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Fri Jan 30 04:41:35 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 30 Jan 2004 09:41:35 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: References: Message-ID: <47066.193.60.81.207.1075455695.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- > I would suggest study some relational database theory > first. The the rest will solve it self afterwards. Ahh, if only it were that simple... > -----Original Message----- > From: BORN II CODE > To: bio_bulletin_board at bioinformatics.org > Sent: 2004-01-28 10:59 > Subject: [BiO BB] Please guide me > > Hi ! i am a still new to bioinformatics.currently i am working on > developing a database with the intergration of xml.as far as i > understand, most of the databanks has its own data(heterogenous > format).what are the fields that i must know in order to develop a database?how > can i retrieve biological data from these databanks.i only know things at the > surface level.many of the articles are very > confusing.as far as i am concern there are things like protein sequence and DNA > sequence.where can i get a sample database table containing field for such > entity?? > > my plan of architecture (architecture for the system which i am going to develop) > consist of a database which will be built using Oracle 9i, XML and SAX parser for > converting various formats into a unified format plus PERL for communicating with > the bio databank's servers. > > please advise if this is feasible or redundant otherwise.i am pretty much > perplexed in determing the right data types for my database.please guide me and i > am not asking anyone of you to develop the systems for me.i am willing to learn > and develop concurrently with advice from you. > > please help me. > > sargunan > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Austin.Tanney at arragen.com Fri Jan 30 05:26:41 2004 From: Austin.Tanney at arragen.com (Austin Tanney) Date: Fri, 30 Jan 2004 10:26:41 -0000 Subject: [BiO BB] Please guide me Message-ID: I agree completely Dan, For example, within the field of genetics, gene names themselves are non-descriptive, and indeed many genes have many different synonyms. This has, of course, led to the development of gene ontology's for use in computer applications to aid the identification of genes computationally. The more we can standardise the methods by which we communicate information, both between ourselves and, more importantly between ourselves and machines, the less time we waste reinventing the wheel. Austin -----Original Message----- From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] Sent: 30 January 2004 09:35 To: bio_bulletin_board at bioinformatics.org Cc: B.A.T.Svensson at lumc.nl Subject: RE: [BiO BB] Please guide me ++ HKG-- >>> What would the benefits of a common schema be? > >>interoperability, foundation of the field, common development >>environment, growth > > A common schem wont help one to achive that. Not directly no - but it would be a big help! Maybe this is a big prejudice of mine, but I am actually quite passionate about this idea. After all, when one mathematician talks to another, they have a common formal language with which to do so - chemists too and the same with comp-sci. Now, while every biologist damn well knows he has a common language to communicate with his peers, this language is not easily formalized. The previous examples are able to work by defining primitives and association rules, but in biology the primitives are already high level concepts, and the association rules are often the results of ongoing research activities. Thus these 'fundamentals' are not easy to agree - this is why we must develop a formal framework within which precise definitions and relationships can emerge pragmatically, in effect leading to a global schema. From the viewpoint of the philosophy of science I think this is how it works in the brains of biologists (I could be wrong), the difficulty is getting something similar to happen in a computer friendly way. I am 100% confident (maybe you see my prejudice) that this will happen someday. Ta, Dan. >>I guess people can add more. > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern Ireland From mgruenb at gmx.net Fri Jan 30 05:29:16 2004 From: mgruenb at gmx.net (Michael Gruenberger) Date: Fri, 30 Jan 2004 10:29:16 +0000 Subject: [BiO BB] Please guide me In-Reply-To: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <1075458556.3020.18.camel@vogel> I can see why the idea of a common language is a good idea, but I don't understand how a schema would achieve that? If you want databases to talk to each other in a common language then you need a common network transport (e.g. web services, XML, SOAP, BioMoby) and a common set of terms or ontologies (e.g. GO, EMAP, MA, MPATH, see http://obo.sourceforge.net/ or http://www.geneontology.org). This would basically allow your databases to talk to each other and I'm sure a common schema would make life easier, but it would be a lot of additional work to integrate this 'global schema' into existing databases. And some if not most of it would be redundant, at least for our database, because we don't for example store information about genes, but simply store the gene name + GO id and then link to other database which have more detailed information. Hmmm... I'd really like to understand your idea though! Could you give an example of how this would work? Cheers, Michael. -- Michael Gruenberger Database developer, Pathbase, http://www.pathbase.net PGP-Public Key ID: 278E1DFF On Fri, 2004-01-30 at 09:34, Dan Bolser wrote: > ++ HKG-- > >>> What would the benefits of a common schema be? > > > >>interoperability, foundation of the field, common development > >>environment, growth > > > > A common schem wont help one to achive that. > > Not directly no - but it would be a big help! > > Maybe this is a big prejudice of mine, but I am actually quite passionate about this > idea. After all, when one mathematician talks to another, they have a common formal > language with which to do so - chemists too and the same with comp-sci. Now, while > every biologist damn well knows he has a common language to communicate with his > peers, this language is not easily formalized. The previous examples are able to > work by defining primitives and association rules, but in biology the primitives are > already high level concepts, and the association rules are often the results of > ongoing research activities. Thus these 'fundamentals' are not easy to agree - this > is why we must develop a formal framework within which precise definitions and > relationships can emerge pragmatically, in effect leading to a global schema. From > the viewpoint of the philosophy of science I think this is how it works in the > brains of biologists (I could be wrong), the difficulty is getting something similar > to happen in a computer friendly way. I am 100% confident (maybe you see my > prejudice) that this will happen someday. > > Ta, > Dan. > > >>I guess people can add more. > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From yyjia at pmail.ntu.edu.sg Fri Jan 30 05:53:00 2004 From: yyjia at pmail.ntu.edu.sg (#JIA YIYU#) Date: Fri, 30 Jan 2004 18:53:00 +0800 Subject: [BiO BB] RE: [Cheminformatics] RE: [BioInformatics Group] alingment matric score for 22 amino acids; Amino acids Cystine and Hyrooxyproline Message-ID: <052033A55521254893A4E2041957E1D09F8A74@mail03.student.main.ntu.edu.sg> Hi Screenu, Thank you very much for your helps! I was confused because I got the 22 number from the textbook "Molecular Biology in Medicine" by Thimothy M. Cox & John Sinclair. This textbook is first pritned in 1997. In page 25, it is said "However, as there are only some 22 amino acids some of the 61 codons specifying amino acids are redundant ...". I was confused because that book is newer than the textbook, which I learnt before. And after i carefully count the number of amino acids in its genetic code table. There are only 20 amino acids there! Thanks a lot! Jia Yiyu -----Original Message----- From: VB Sreenu [mailto:sreenu at cdfd.org.in] Sent: Friday, January 30, 2004 5:26 PM To: cheminformatics at yahoogroups.com Cc: BioInformaticsGroup at yahoogroups.com Subject: Re: [Cheminformatics] RE: [BioInformatics Group] alingment matric score for 22 amino acids; Amino acids Cystine and Hyrooxyproline Hi Jia, cystine and hydroxyproline were considered as unusual amino acids in the proteins before the discovery of post translational modifications. That is the reason they were established in old biochemistry books as extra amino acids. Genetic code is not 100% universal. As u said, organelle genetic code is different from organisms genetic code. selenocystine was found in the organism's proteins (single letter amino acid code is "U"). some examples are (all from E. coli only) formate dehydrogenase-N, nitrate-inducible, alpha subunit [Escherichia coli K12] ac number 16129433. formate dehydrogenase-O, major subunit [Escherichia coli K12] ac number is 16131734 selenopolypeptide subunit of formate dehydrogenase H [Escherichia coli K12] ac number 16131905 from those examples it is very clear that selenocystine should have a crucial role in the function of formate dehydrogenase. (I dont have information on this) you can calculate a substitution matrix including selenocystine proteins. But that might not be statistically significant. Because available selenocystine containing proteins are very few. regards Sreenu ----------------------------- VB Sreenu Research scholar Laboratory of Computational Biology CDFD, Nacharam, Hyderabad-76 India #JIA YIYU# wrote: >Hi, > >Thank you for your information. But I still feel strange that why only Cystine and Hyrooxyproline are particularly point out because there are not only two modified amino acids. > >About Selenocystine, its condon is UGA, which is normally reconganized as stop condon (except in chondriosome). So is Selenocystine found in particular organism or organelle ? May I have more detail information about it? > >Best regards! > > Jia Yiyu > > #JIA YIYU# wrote: > > Hi there, > > Anybody would kindly point out where the protein alingment matrix > score for 22 nmino acids can be found? > > According to some old biochemistry textbook, all known proteins and > enzymes are all produced from only 20 amino acids. But some new books > declare that there actually 22 amino acids discovered so far. Have > these 22 amino acids been popular accepted? It seems the extra two > amino acids are Cystine and Hyrooxyproline. Any expert would like to > give out more information on them? > > Thanks in advance! > > Best regards! > > Jia Yiyu > > ========================================= > * > * Mr. Jia Yiyu > * > * Email : yyjia at pmail.ntu.edu.sg > * Web : http://birc.ntu.edu.sg/yyjia > * > * Address: > * Bioinformatics Research Centre (BIRC) > * Research TechnoPlaza > * 3rd Storey, XFrontiers Block > * 50 Nanyang Avenue > * Singapore 637553 > * > * Fax: (65) 6316-2780 > ======================================= > > > ------------------------------------------------------------------------ > *Yahoo! Groups Links* > > * To visit your group on the web, go to: > http://groups.yahoo.com/group/BioInformaticsGroup/ > > * To unsubscribe from this group, send an email to: > BioInformaticsGroup-unsubscribe at yahoogroups.com > > > * Your use of Yahoo! Groups is subject to the Yahoo! Terms of > Service . > > ------------------------ Yahoo! Groups Sponsor ---------------------~--> Buy Ink Cartridges or Refill Kits for your HP, Epson, Canon or Lexmark Printer at MyInks.com. Free s/h on orders $50 or more to the US & Canada. http://www.c1tracking.com/l.asp?cid=5511 http://us.click.yahoo.com/mOAaAA/3exGAA/qnsNAA/efDslB/TM ---------------------------------------------------------------------~-> Yahoo! Groups Links To visit your group on the web, go to: http://groups.yahoo.com/group/BioInformaticsGroup/ To unsubscribe from this group, send an email to: BioInformaticsGroup-unsubscribe at yahoogroups.com Your use of Yahoo! Groups is subject to: http://docs.yahoo.com/info/terms/ From obj at obj.hopto.org Fri Jan 30 07:53:13 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 14:53:13 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <1075458556.3020.18.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> Message-ID: <401A53B9.8050709@obj.hopto.org> Michael Gruenberger wrote: >I can see why the idea of a common language is a good idea, but I don't >understand how a schema would achieve that? > > when i was mentioning common schema i wasn't considering database schema (structure). such global database schema won't make sense since everyone may have different requirements. i meant common schema as a common communication protocol. yes, it's not a right word, it came from web services, xml schema, etc. and yes, new bioinformatics language would make lot more for community. indeed, i see some confusion about why should every bioinformatician use perl (well, perl comes first when you ask google)... nor it's designed for it, nor it make learning path easier (time to come and do research). i think the new language should be developed, language which makes good string processing as perl does and introduces constructs/objects which are familiar for people with biological background. > >If you want databases to talk to each other in a common language then >you need a common network transport (e.g. web services, XML, SOAP, >BioMoby) and a common set of terms or ontologies (e.g. GO, EMAP, MA, >MPATH, see http://obo.sourceforge.net/ or http://www.geneontology.org). > >This would basically allow your databases to talk to each other and I'm >sure a common schema would make life easier, but it would be a lot of >additional work to integrate this 'global schema' into existing >databases. And some if not most of it would be redundant, at least for >our database, because we don't for example store information about >genes, but simply store the gene name + GO id and then link to other >database which have more detailed information. > >Hmmm... I'd really like to understand your idea though! Could you give >an example of how this would work? > >Cheers, > >Michael. > > > From mgruenb at gmx.net Fri Jan 30 06:13:07 2004 From: mgruenb at gmx.net (Michael Gruenberger) Date: Fri, 30 Jan 2004 11:13:07 +0000 Subject: [BiO BB] Please guide me In-Reply-To: <401A53B9.8050709@obj.hopto.org> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> Message-ID: <1075461187.3013.28.camel@vogel> On Fri, 2004-01-30 at 12:53, Andrius wrote: > when i was mentioning common schema i wasn't considering database schema > (structure). such global database > schema won't make sense since everyone may have different requirements. > i meant common schema as a common communication > protocol. yes, it's not a right word, it came from web services, xml > schema, Oh sorry I misunderstood you. A common XML schema would indeed be quite interesting, but still different databases would have very different needs and I'm not sure if it would be feasible... > etc. and yes, new bioinformatics language would make > lot more for community. indeed, i see some confusion about why should > every bioinformatician use perl (well, perl comes first when you ask > google)... nor it's designed for it, nor it make learning path easier > (time to come and do research). i think the new language should be > developed, language which makes good string processing as perl does and > introduces constructs/objects which are familiar for people with > biological background. > > > So you mean something like Mathematica for Bioinformatics. Yes, I guess that would be useful, but what would it do that BioPerl or BioJava can't do? You have the advantage that programmers already know Perl of Java and can just plug in the new API's for bioinformatics. A bioinformatics language would have a much steeper learning curve, so it would have to offer some considerable advantages. Cheers, Michael. -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From obj at obj.hopto.org Fri Jan 30 08:37:59 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 15:37:59 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <1075461187.3013.28.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> Message-ID: <401A5E37.5080301@obj.hopto.org> Michael Gruenberger wrote: >On Fri, 2004-01-30 at 12:53, Andrius wrote: > > > >>when i was mentioning common schema i wasn't considering database schema >>(structure). such global database >>schema won't make sense since everyone may have different requirements. >>i meant common schema as a common communication >>protocol. yes, it's not a right word, it came from web services, xml >>schema, >> >> > > >Oh sorry I misunderstood you. A common XML schema would indeed be quite >interesting, but still different databases would have very different >needs and I'm not sure if it would be feasible... > > > i was still talking about using xml derived from common xml schemas for communication purposes. anyway, i still haven't done a concise reasearch of bioinformatics tools and can't say if something is already implemented, it may. > > >>etc. and yes, new bioinformatics language would make >>lot more for community. indeed, i see some confusion about why should >>every bioinformatician use perl (well, perl comes first when you ask >>google)... nor it's designed for it, nor it make learning path easier >>(time to come and do research). i think the new language should be >>developed, language which makes good string processing as perl does and >>introduces constructs/objects which are familiar for people with >>biological background. >> >> >> > > > >So you mean something like Mathematica for Bioinformatics. Yes, I guess >that would be useful, but what would it do that BioPerl or BioJava can't >do? You have the advantage that programmers already know Perl of Java >and can just plug in the new API's for bioinformatics. A bioinformatics >language would have a much steeper learning curve, so it would have to >offer some considerable advantages. > > i'm looking forward for scientists to have research tools such as programming languages for their specific field so everyone could develop their own research routines and systems. commercial packets are too closed for this. we need java for bioinformaticians, but it should be independant of java (or any other general programming language) , because java expresses too much of object oriented programming, constructs which confuse researcher without computer science background. i want all (at least researchers) to be programmers, because full computational potential can be grasped having a right customizable tool ( such as programming language). i just have some intuition and if you have something to add i'll be happy to hear. Cheers, Andrius From B.A.T.Svensson at lumc.nl Fri Jan 30 06:40:44 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 30 Jan 2004 12:40:44 +0100 Subject: [BiO BB] Please guide me Message-ID: >>>> What would the benefits of a common schema be? >>> >>> interoperability, foundation of the field, common >>> development environment, growth >> >> A common schem wont help one to achive that. > Not directly no - but it would be a big help! The problem with a common schema is that it will create much more problem then it ever will be able to solves. It is simply a bad idea! A common communication interface between databases is on the other hand a good idea. From Austin.Tanney at arragen.com Fri Jan 30 06:50:03 2004 From: Austin.Tanney at arragen.com (Austin Tanney) Date: Fri, 30 Jan 2004 11:50:03 -0000 Subject: [BiO BB] Please guide me Message-ID: -----Original Message----- >The problem with a common schema is that it will create >much more problem then it ever will be able to solves. I dont disagree with this, but I would be interested in knowing why you think this is the case? Austin This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern Ireland From mgruenb at gmx.net Fri Jan 30 07:16:07 2004 From: mgruenb at gmx.net (Michael Gruenberger) Date: Fri, 30 Jan 2004 12:16:07 +0000 Subject: [BiO BB] Please guide me In-Reply-To: <401A5E37.5080301@obj.hopto.org> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> Message-ID: <1075464967.3012.43.camel@vogel> On Fri, 2004-01-30 at 13:37, Andrius wrote: > i was still talking about using xml derived from common xml schemas for > communication purposes. anyway, i still > haven't done a concise reasearch of bioinformatics tools and can't say > if something is already implemented, it may. > So was I. My point was that different databases have very different data sets and it would be difficult to find a common xml schema. SOAP seems to be a much better way forward (than plain XML + XML Schema), because you can customise it much more towards different needs and you don't have to agree on a common schema. It also seems to be what most databases are implementing at the moment (see BioMoby).... > i'm looking forward for scientists to have research tools such as > programming languages for their > specific field so everyone could develop their own research routines and > systems. commercial packets > are too closed for this. we need java for bioinformaticians, but it > should be independant of java (or any other > general programming language) , because java expresses too much of > object oriented programming, constructs which confuse researcher without > computer science background. i want all (at least researchers) to be > programmers, because full computational potential can be > grasped having a right customizable tool ( such as programming > language). i just have some intuition and if you have something > to add i'll be happy to hear. Well... in an ideal world... but in my experience there are two kinds of researchers: The one's who are really into computers and know a couple of programming languages and wouldn't mind learning Java. The other kind (the majority) is those who can use web interfaces, but don't really want to know anything more about computers and wouldn't want to learn even a really simple language. So it's a good idea, but is there a 'market' for it? Cheers, Michael. -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From dmb at mrc-dunn.cam.ac.uk Fri Jan 30 07:30:14 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 30 Jan 2004 12:30:14 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: <401A53B9.8050709@obj.hopto.org> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> Message-ID: <49264.193.60.81.207.1075465814.squirrel@www.mrc-dunn.cam.ac.uk> PERL = Protein Engineering Research Language ;) ++ Andrius-- > Michael Gruenberger wrote: > >>I can see why the idea of a common language is a good idea, but I don't >> understand how a schema would achieve that? >> >> > when i was mentioning common schema i wasn't considering database schema > (structure). such global database > schema won't make sense since everyone may have different requirements. i meant > common schema as a common communication > protocol. yes, it's not a right word, it came from web services, xml schema, etc. > and yes, new bioinformatics language would make > lot more for community. indeed, i see some confusion about why should every > bioinformatician use perl (well, perl comes first when you ask google)... nor > it's designed for it, nor it make learning path easier (time to come and do > research). i think the new language should be developed, language which makes good > string processing as perl does and introduces constructs/objects which are > familiar for people with > biological background. > >> >>If you want databases to talk to each other in a common language then you need a >> common network transport (e.g. web services, XML, SOAP, BioMoby) and a common set >> of terms or ontologies (e.g. GO, EMAP, MA, MPATH, see http://obo.sourceforge.net/ >> or http://www.geneontology.org). >> >>This would basically allow your databases to talk to each other and I'm sure a >> common schema would make life easier, but it would be a lot of additional work to >> integrate this 'global schema' into existing >>databases. And some if not most of it would be redundant, at least for our >> database, because we don't for example store information about genes, but simply >> store the gene name + GO id and then link to other database which have more >> detailed information. >> >>Hmmm... I'd really like to understand your idea though! Could you give an example >> of how this would work? >> >>Cheers, >> >>Michael. >> >> >> > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From B.A.T.Svensson at lumc.nl Fri Jan 30 08:47:13 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 30 Jan 2004 14:47:13 +0100 Subject: [BiO BB] Please guide me Message-ID: >> The problem with a common schema is that it will create >> much more problem then it ever will be able to solves. > I dont disagree with this, but I would be interested > in knowing why you think this is the case? Why are million and millions of dollars spent every year on changes in databases system all around the world? From dmb at mrc-dunn.cam.ac.uk Fri Jan 30 08:27:26 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 30 Jan 2004 13:27:26 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: References: Message-ID: <49967.193.60.81.207.1075469246.squirrel@www.mrc-dunn.cam.ac.uk> ++ HKG-- >>>>> What would the benefits of a common schema be? >>>> >>>> interoperability, foundation of the field, common >>>> development environment, growth >>> >>> A common schem wont help one to achive that. > >> Not directly no - but it would be a big help! > > The problem with a common schema is that it will create > much more problem then it ever will be able to solves. > > It is simply a bad idea! A common communication interface > between databases is on the other hand a good idea. Yes, but not if you don't know what you are communicating... Sorry I think I have fallen into the trap of using the term schema inappropriatly too... and global or centralized is the wrong term too... > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From obj at obj.hopto.org Fri Jan 30 10:20:36 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 17:20:36 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <1075464967.3012.43.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> Message-ID: <401A7644.4020602@obj.hopto.org> Michael Gruenberger wrote: >On Fri, 2004-01-30 at 13:37, Andrius wrote: > > > >>i was still talking about using xml derived from common xml schemas for >>communication purposes. anyway, i still >>haven't done a concise reasearch of bioinformatics tools and can't say >>if something is already implemented, it may. >> >> >> > >So was I. My point was that different databases have very different data >sets and it would be difficult to find a common xml schema. SOAP seems >to be a much better way forward (than plain XML + XML Schema), because >you can customise it much more towards different needs and you don't >have to agree on a common schema. It also seems to be what most >databases are implementing at the moment (see BioMoby).... > > > >>i'm looking forward for scientists to have research tools such as >>programming languages for their >>specific field so everyone could develop their own research routines and >>systems. commercial packets >>are too closed for this. we need java for bioinformaticians, but it >>should be independant of java (or any other >>general programming language) , because java expresses too much of >>object oriented programming, constructs which confuse researcher without >>computer science background. i want all (at least researchers) to be >>programmers, because full computational potential can be >>grasped having a right customizable tool ( such as programming >>language). i just have some intuition and if you have something >>to add i'll be happy to hear. >> >> > >Well... in an ideal world... but in my experience there are two kinds of >researchers: The one's who are really into computers and know a couple >of programming languages and wouldn't mind learning Java. The other kind >(the majority) is those who can use web interfaces, but don't really >want to know anything more about computers and wouldn't want to learn >even a really simple language. So it's a good idea, but is there a >'market' for it? > > > i'm sure real world will demand it. it's kind of a feeling when you doing research with such tools..it reminds me open source climate a lot. the thing is... sometimes even programmers do not think in a real way. they tend to follow 'practices' and there's little few who follows their brain. you may disagree and of course i can ask: does our today 'market' demand thinking? same for research i think. as long as researchers demand tools which allow them to think free ( and gain better results this way ) there's a market for such tools. of course it may not be mainstream, but there's nothing wrong with that. i'm not much familiar with research routines (i'm still graduating for bachelor) and people in it, but i have few friends there. they tend to say that even in academic world there's a lot of serial writing (i mean writing papers just to increase curriculum) and there's no surprise such people do not demand open thinking tools. and there's nothing wrong with that again:) as long as there's bunch of people who care about a quality of their work (research). Cheers, Andrius >Cheers, > >Michael. > > > From mgruenb at gmx.net Fri Jan 30 09:19:40 2004 From: mgruenb at gmx.net (Michael Gruenberger) Date: Fri, 30 Jan 2004 14:19:40 +0000 Subject: [BiO BB] Please guide me In-Reply-To: <401A7644.4020602@obj.hopto.org> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> <401A7644.4020602@obj.hopto.org> Message-ID: <1075472380.3013.62.camel@vogel> On Fri, 2004-01-30 at 15:20, Andrius wrote: > > > i'm sure real world will demand it. it's kind of a feeling when you > doing research with such tools..it > reminds me open source climate a lot. the thing is... sometimes even > programmers do not think in a real way. > they tend to follow 'practices' and there's little few who follows their > brain. you may disagree and of course i can ask: > does our today 'market' demand thinking? same for research i think. as > long as researchers demand tools which > allow them to think free ( and gain better results this way ) there's a > market for such tools. of course it may not be mainstream, > but there's nothing wrong with that. i'm not much familiar with research > routines (i'm still graduating for bachelor) and people in it, but i > have few friends there. they tend to say that even in academic world > there's a lot of serial writing (i mean writing papers just to increase > curriculum) and there's no surprise such people do not demand open > thinking tools. and there's nothing wrong with that again:) as long as > there's bunch of people who care about a quality of their work (research). Yes, you are right, researchers need (computer) tools, but they need to be very easy to use and a new programming language would also have to be very easy to use. What would your bio-language look like? What would make it easier to use than existing BioJava or BioPerl? Bioinformatics is a very wide field (I work on two projects at the moment, one is mainly database stuff, the other one 3D images). What would your language focus on? Michael. -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From B.A.T.Svensson at lumc.nl Fri Jan 30 09:24:01 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 30 Jan 2004 15:24:01 +0100 Subject: [BiO BB] Please guide me Message-ID: > The problem with a common schema is that it will create > much more problem then it ever will be able to solves. > > It is simply a bad idea! A common communication interface > between databases is on the other hand a good idea. > Yes, but not if you don't know what you are communicating... I do not understand what you are trying to say here? From obj at obj.hopto.org Fri Jan 30 11:37:32 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 18:37:32 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <1075472380.3013.62.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> <401A7644.4020602@obj.hopto.org> <1075472380.3013.62.camel@vogel> Message-ID: <401A884C.8070001@obj.hopto.org> Michael Gruenberger wrote: >On Fri, 2004-01-30 at 15:20, Andrius wrote: > > > >>i'm sure real world will demand it. it's kind of a feeling when you >>doing research with such tools..it >>reminds me open source climate a lot. the thing is... sometimes even >>programmers do not think in a real way. >>they tend to follow 'practices' and there's little few who follows their >>brain. you may disagree and of course i can ask: >>does our today 'market' demand thinking? same for research i think. as >>long as researchers demand tools which >>allow them to think free ( and gain better results this way ) there's a >>market for such tools. of course it may not be mainstream, >>but there's nothing wrong with that. i'm not much familiar with research >>routines (i'm still graduating for bachelor) and people in it, but i >>have few friends there. they tend to say that even in academic world >>there's a lot of serial writing (i mean writing papers just to increase >>curriculum) and there's no surprise such people do not demand open >>thinking tools. and there's nothing wrong with that again:) as long as >>there's bunch of people who care about a quality of their work (research). >> >> > >Yes, you are right, researchers need (computer) tools, but they need to >be very easy to use and a new programming language would also have to be >very easy to use. What would your bio-language look like? What would >make it easier to use than existing BioJava or BioPerl? Bioinformatics >is a very wide field (I work on two projects at the moment, one is >mainly database stuff, the other one 3D images). What would your >language focus on? > > it may be pluggable, but i don't want to speculate. i just have an idea for a future. in short we can build language for JVM for example which uses all what Java ( notice 3d here too) can provide but completely hiddens it from bioinformatics programmer. i'm sure i'll find problems with existing solutions (bioperl and biojava) when i put my hands on it. and yes, ease of use is a main reason for such custom language. and i guess it means how language is presented for a researcher. i doubt plain java is applicable. >Michael. > > From obj at obj.hopto.org Fri Jan 30 12:07:39 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 19:07:39 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <1075472380.3013.62.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> <401A7644.4020602@obj.hopto.org> <1075472380.3013.62.camel@vogel> Message-ID: <401A8F5B.9090403@obj.hopto.org> Michael Gruenberger wrote: >On Fri, 2004-01-30 at 15:20, Andrius wrote: > > > >>i'm sure real world will demand it. it's kind of a feeling when you >>doing research with such tools..it >>reminds me open source climate a lot. the thing is... sometimes even >>programmers do not think in a real way. >>they tend to follow 'practices' and there's little few who follows their >>brain. you may disagree and of course i can ask: >>does our today 'market' demand thinking? same for research i think. as >>long as researchers demand tools which >>allow them to think free ( and gain better results this way ) there's a >>market for such tools. of course it may not be mainstream, >>but there's nothing wrong with that. i'm not much familiar with research >>routines (i'm still graduating for bachelor) and people in it, but i >>have few friends there. they tend to say that even in academic world >>there's a lot of serial writing (i mean writing papers just to increase >>curriculum) and there's no surprise such people do not demand open >>thinking tools. and there's nothing wrong with that again:) as long as >>there's bunch of people who care about a quality of their work (research). >> >> > >Yes, you are right, researchers need (computer) tools, but they need to >be very easy to use and a new programming language would also have to be >very easy to use. What would your bio-language look like? What would >make it easier to use than existing BioJava or BioPerl? Bioinformatics >is a very wide field (I work on two projects at the moment, one is >mainly database stuff, the other one 3D images). What would your >language focus on? > >Michael. > > but perhaps you're right. biojava makes huge sense. just the fact that plain java is used makes a bit unconfortable for a researcher to come up quickly. but no alternative for now. From mgruenb at gmx.net Fri Jan 30 10:24:21 2004 From: mgruenb at gmx.net (Michael Gruenberger) Date: Fri, 30 Jan 2004 15:24:21 +0000 Subject: [BiO BB] Please guide me In-Reply-To: <401A8F5B.9090403@obj.hopto.org> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> <401A7644.4020602@obj.hopto.org> <1075472380.3013.62.camel@vogel> <401A8F5B.9090403@obj.hopto.org> Message-ID: <1075476261.3017.65.camel@vogel> well... good luck with your search and thanks for the interesting discussion! Michael. > > > but perhaps you're right. biojava makes huge sense. just the fact that > plain java is used makes > a bit unconfortable for a researcher to come up quickly. but no > alternative for now. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From obj at obj.hopto.org Fri Jan 30 12:31:06 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 19:31:06 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <1075476261.3017.65.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> <401A7644.4020602@obj.hopto.org> <1075472380.3013.62.camel@vogel> <401A8F5B.9090403@obj.hopto.org> <1075476261.3017.65.camel@vogel> Message-ID: <401A94DA.9080209@obj.hopto.org> Michael Gruenberger wrote: >well... good luck with your search and thanks for the interesting >discussion! > > thank you. >Michael. > > >>but perhaps you're right. biojava makes huge sense. just the fact that >>plain java is used makes >>a bit unconfortable for a researcher to come up quickly. but no >>alternative for now. >> >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_boar >> >d > > From obj at obj.hopto.org Fri Jan 30 11:47:37 2004 From: obj at obj.hopto.org (Andrius) Date: Fri, 30 Jan 2004 18:47:37 +0200 Subject: [BiO BB] Please guide me In-Reply-To: <1075472380.3013.62.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> <401A7644.4020602@obj.hopto.org> <1075472380.3013.62.camel@vogel> Message-ID: <401A8AA9.1060404@obj.hopto.org> Michael Gruenberger wrote: >On Fri, 2004-01-30 at 15:20, Andrius wrote: > > > >>i'm sure real world will demand it. it's kind of a feeling when you >>doing research with such tools..it >>reminds me open source climate a lot. the thing is... sometimes even >>programmers do not think in a real way. >>they tend to follow 'practices' and there's little few who follows their >>brain. you may disagree and of course i can ask: >>does our today 'market' demand thinking? same for research i think. as >>long as researchers demand tools which >>allow them to think free ( and gain better results this way ) there's a >>market for such tools. of course it may not be mainstream, >>but there's nothing wrong with that. i'm not much familiar with research >>routines (i'm still graduating for bachelor) and people in it, but i >>have few friends there. they tend to say that even in academic world >>there's a lot of serial writing (i mean writing papers just to increase >>curriculum) and there's no surprise such people do not demand open >>thinking tools. and there's nothing wrong with that again:) as long as >>there's bunch of people who care about a quality of their work (research). >> >> > >Yes, you are right, researchers need (computer) tools, but they need to >be very easy to use and a new programming language would also have to be >very easy to use. What would your bio-language look like? What would >make it easier to use than existing BioJava or BioPerl? Bioinformatics >is a very wide field (I work on two projects at the moment, one is >mainly database stuff, the other one 3D images). What would your >language focus on? > > it may be pluggable, but i don't want to speculate. i just have an idea for a future. in short we can build language for JVM for example which uses all what Java ( notice 3d here too) can provide but completely hiddens it from bioinformatics programmer. i'm sure i'll find problems with existing solutions (bioperl and biojava) when i put my hands on it. and yes, ease of use is a main reason for such custom language. and i guess it means how language is presented for a researcher. i doubt plain java is applicable. >Michael. > > From dmb at mrc-dunn.cam.ac.uk Fri Jan 30 15:28:26 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 30 Jan 2004 20:28:26 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: <401A884C.8070001@obj.hopto.org> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> <1075461187.3013.28.camel@vogel> <401A5E37.5080301@obj.hopto.org> <1075464967.3012.43.camel@vogel> <401A7644.4020602@obj.hopto.org> <1075472380.3013.62.camel@vogel> <401A884C.8070001@obj.hopto.org> Message-ID: <55423.193.60.81.207.1075494506.squirrel@www.mrc-dunn.cam.ac.uk> ++ Andrius-- > Michael Gruenberger wrote: > >>On Fri, 2004-01-30 at 15:20, Andrius wrote: >> >> >> >>>i'm sure real world will demand it. it's kind of a feeling when you doing >>> research with such tools..it >>>reminds me open source climate a lot. the thing is... sometimes even >>> programmers do not think in a real way. >>>they tend to follow 'practices' and there's little few who follows their brain. >>> you may disagree and of course i can ask: >>>does our today 'market' demand thinking? same for research i think. as long as >>> researchers demand tools which >>>allow them to think free ( and gain better results this way ) there's a market >>> for such tools. of course it may not be mainstream, >>>but there's nothing wrong with that. i'm not much familiar with research >>> routines (i'm still graduating for bachelor) and people in it, but i have few >>> friends there. they tend to say that even in academic world there's a lot of >>> serial writing (i mean writing papers just to increase curriculum) and there's >>> no surprise such people do not demand open thinking tools. and there's nothing >>> wrong with that again:) as long as there's bunch of people who care about a >>> quality of their work (research). >>> >>> >> >>Yes, you are right, researchers need (computer) tools, but they need to be very >> easy to use and a new programming language would also have to be very easy to >> use. What would your bio-language look like? What would make it easier to use >> than existing BioJava or BioPerl? Bioinformatics is a very wide field (I work on >> two projects at the moment, one is mainly database stuff, the other one 3D >> images). What would your >>language focus on? >> >> > it may be pluggable, but i don't want to speculate. i just have an idea for a > future. in short > we can build language for JVM for example which uses all what Java ( notice 3d > here too) can provide but completely hiddens it from > bioinformatics programmer. i'm sure i'll find problems with existing solutions > (bioperl and biojava) when i put my hands on it. and yes, ease of use is a main > reason for such custom language. and i guess it means how language is presented > for a researcher. i doubt > plain java is applicable. sounds like the tower of babel gone wrong - java, perl, c, all are good for bioinformatics, laying the concepts on top is the tricky part, and the more you ask a language to do for you, the more 'locked in' to a particular mind set you get. Traditional programing languages are good because of the freedom of they give - beyond that it is a matter of taste. I do not think each dicipline of science should have its own language. subroutines yes, dialect no. >>Michael. >> >> > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Fri Jan 30 15:45:33 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 30 Jan 2004 20:45:33 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: <1075458556.3020.18.camel@vogel> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> Message-ID: <55645.193.60.81.207.1075495533.squirrel@www.mrc-dunn.cam.ac.uk> ++ Michael Gruenberger-- > I can see why the idea of a common language is a good idea, but I don't understand > how a schema would achieve that? > > > If you want databases to talk to each other in a common language then you need a > common network transport (e.g. web services, XML, SOAP, BioMoby) and a common set > of terms or ontologies (e.g. GO, EMAP, MA, MPATH, see http://obo.sourceforge.net/ > or http://www.geneontology.org). Thanks for the link. > This would basically allow your databases to talk to each other and I'm sure a > common schema would make life easier, but it would be a lot of additional work to > integrate this 'global schema' into existing > databases. And some if not most of it would be redundant, at least for our > database, because we don't for example store information about genes, but simply > store the gene name + GO id and then link to other database which have more > detailed information. Schemas (or more generally data models) provide context for data. Rather than simply enumerating the symbolic links between data, a data model hopes to organize the data conceptually, providing semantic meaning to abstract objects. You are absolutely right that a 'global schema' is more than most people need and is hard to agree on or implement. What I mean is a bunch of independent schema's (schemata?) which can interoperate through common terms (ontologies as you put it). No one researcher can ever decide on the data model for his data, because making a model implies understanding the field - which negates the process of research. This is why each researcher should develope independent sub models (modlets?) for the data they work on, within a machine readable format to allow computer scientists to interoperate between schemata. > Hmmm... I'd really like to understand your idea though! Could you give an example > of how this would work? In the simplest terms, I imagine a wet lab working on mitochondrial transporter proteins. Because of their work, they develope a database of mitochondirial transporter proteins. Then are (probably) the most qualified people in the world to make this database, so (much in the way of DAS), they annotate their database as - proteins - mitochondrial - transporters ... within the framework I imagine, that is all that is needed - ontological mappings allow this data to be integrated into a 'global schema', but it is up to the individual researcher as to which labs (data sources) he trusts, and eventually a common consensus will emerge. This is the way science works. Sorry for the slightly garbled response, > > Cheers, > > Michael. > > -- > Michael Gruenberger > Database developer, Pathbase, http://www.pathbase.net > PGP-Public Key ID: 278E1DFF > > > > On Fri, 2004-01-30 at 09:34, Dan Bolser wrote: >> ++ HKG-- >> >>> What would the benefits of a common schema be? >> > >> >>interoperability, foundation of the field, common development >> >>environment, growth >> > >> > A common schem wont help one to achive that. >> >> Not directly no - but it would be a big help! >> >> Maybe this is a big prejudice of mine, but I am actually quite passionate about >> this idea. After all, when one mathematician talks to another, they have a >> common formal language with which to do so - chemists too and the same with >> comp-sci. Now, while every biologist damn well knows he has a common language to >> communicate with his peers, this language is not easily formalized. The previous >> examples are able to work by defining primitives and association rules, but in >> biology the primitives are already high level concepts, and the association >> rules are often the results of ongoing research activities. Thus these >> 'fundamentals' are not easy to agree - this is why we must develop a formal >> framework within which precise definitions and relationships can emerge >> pragmatically, in effect leading to a global schema. From the viewpoint of the >> philosophy of science I think this is how it works in the brains of biologists >> (I could be wrong), the difficulty is getting something similar to happen in a >> computer friendly way. I am 100% confident (maybe you see my prejudice) that >> this will happen someday. >> >> Ta, >> Dan. >> >> >>I guess people can add more. >> > _______________________________________________ >> > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From nchandra at physics.iisc.ernet.in Fri Jan 30 21:44:03 2004 From: nchandra at physics.iisc.ernet.in (Dr.Nagasuma Chandra) Date: Sat, 31 Jan 2004 08:14:03 +0530 (IST) Subject: [BiO BB] Small molecule databases In-Reply-To: <052033A55521254893A4E2041957E1D09F8A74@mail03.student.main.ntu.edu.sg> Message-ID: Hi We are trying to get a database of the three-dimensional structures of small molecules that are already synthesized and available (for eg., in SIGMA/ALDRICH etc), as a supplement to the CSD database, which we have. Any help regarding the websites containing some information and distributors dealing with this will be greatly appreciated. Cheers *********************************************** Dr. Nagasuma Chandra Bioinformatics centre Indian Institute of Science Bangalore 560 012 Tel: +91-80-3092469 or 3601409 Fax: +91-80-3600551 e-mail: nchandra at physics.iisc.ernet.in *********************************************** From dmb at mrc-dunn.cam.ac.uk Sat Jan 31 07:12:48 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 31 Jan 2004 12:12:48 -0000 (GMT) Subject: [BiO BB] Small molecule databases In-Reply-To: References: <052033A55521254893A4E2041957E1D09F8A74@mail03.student.main.ntu.edu.sg> Message-ID: <33451.213.107.104.171.1075551168.squirrel@www.mrc-dunn.cam.ac.uk> ++ Dr.Nagasuma Chandra-- > > Hi > > We are trying to get a database of the three-dimensional structures of > small molecules that are already synthesized and available (for eg., in > SIGMA/ALDRICH etc), as a supplement to the CSD database, which we have. Any help > regarding the websites containing some information and > distributors dealing with this will be greatly appreciated. There is a (or *the*?) ligand database at KEGG http://www.genome.ad.jp/kegg/kegg2.html One (available for download?) at BRENDA http://www.brenda.uni-koeln.de/ You can get details of small molecules (hetero atoms) in the structures of the PDB from PDB SUM http://www.biochem.ucl.ac.uk/bsm/pdbsum/ligands/ And the same data (in a different (cleaner?) form) can be sniffed from the MSD site http://www.ebi.ac.uk/msd-srv/chempdb/cgi-bin/cgi.pl However, I always thought CSD was most comprehensive (but it was not free!). Looking through my googles I saw this http://www.netsci.org/Resources/Web/small.html I once did a small project with Jim Austin at the University of York, he was working on ligand matching using novel hardware (at that time simulated in software). Performance Evaluation of a Fast Chemical Matching Method using Distributed Neural Relaxation, A.Turner and J. Austin, Proceedings of: Fourth International Conference on Knowledge-Based Intelligent Engineering Systems and Allied Technologies (KES'2000), Vol. 1, pp.201-204, Sept 2000. Which is in effect holographic memory, which I always thought was cool. - Nothing to do with my project with him though! You can find his research pages on the university of York (UK) website. Anybody know of a 'structural classification of ligands' (SCOL) data base? I think this would be a great project. Ta, Dan. > Cheers > *********************************************** > Dr. Nagasuma Chandra > Bioinformatics centre > Indian Institute of Science > Bangalore 560 012 > Tel: +91-80-3092469 or 3601409 > Fax: +91-80-3600551 > e-mail: nchandra at physics.iisc.ernet.in > *********************************************** > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeffrey_chang at stanfordalumni.org Fri Jan 30 08:49:14 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Fri, 30 Jan 2004 08:49:14 -0500 Subject: [BiO BB] Please guide me In-Reply-To: <401A53B9.8050709@obj.hopto.org> References: <46955.193.60.81.207.1075455286.squirrel@www.mrc-dunn.cam.ac.uk> <1075458556.3020.18.camel@vogel> <401A53B9.8050709@obj.hopto.org> Message-ID: <174DC680-532B-11D8-901B-000A956845CE@stanfordalumni.org> On Jan 30, 2004, at 7:53 AM, Andrius wrote: > new bioinformatics language would make > lot more for community. indeed, i see some confusion about why should > every bioinformatician use perl (well, perl comes first when you ask > google)... nor it's designed for it, nor it make learning path easier > (time to come and do research). i think the new language should be > developed, language which makes good string processing as perl does > and introduces constructs/objects which are familiar for people with > biological background. You should look into Darwin then: http://cbrg.inf.ethz.ch/Darwin/index.html It's a programming language invented for bioinformatics applications. I've been meaning to look at it. I'm interesting in how this language compares to a general high-level language like Python or Perl, with a robust bioinformatics library (biopython or bioperl). Does anyone have experiences with this and can share them? Jeff From krrupesh at yahoo.com Sat Jan 31 14:28:40 2004 From: krrupesh at yahoo.com (=?iso-8859-1?q?K.=20R.=20Rupesh?=) Date: Sat, 31 Jan 2004 19:28:40 +0000 (GMT) Subject: [BiO BB] Re: [Cheminformatics] Small molecule databases In-Reply-To: Message-ID: <20040131192840.52706.qmail@web41806.mail.yahoo.com> Dear Dr. Nagasuma Chandra, Hope this few links might help you for your database. http://www.nyu.edu/pages/mathmol/library/ http://ligand-depot.rutgers.edu/LigandDepot/jsp/BrowseHandler.jsp?BrowseBy=2 http://www.ccp4.ac.uk/ http://cmm.info.nih.gov/modeling/databases_body.html http://journals.iucr.org/sincris-top/themes/chimie/ Good luck, Rupesh "Dr.Nagasuma Chandra" wrote: Hi We are trying to get a database of the three-dimensional structures of small molecules that are already synthesized and available (for eg., in SIGMA/ALDRICH etc), as a supplement to the CSD database, which we have. Any help regarding the websites containing some information and distributors dealing with this will be greatly appreciated. Cheers *********************************************** Dr. Nagasuma Chandra Bioinformatics centre Indian Institute of Science Bangalore 560 012 Tel: +91-80-3092469 or 3601409 Fax: +91-80-3600551 e-mail: nchandra at physics.iisc.ernet.in *********************************************** ********* Great your standing at the crossroads of Chemistry and Computer technology ********* Yahoo! Groups SponsorADVERTISEMENT --------------------------------- Yahoo! Groups Links To visit your group on the web, go to: http://groups.yahoo.com/group/cheminformatics/ To unsubscribe from this group, send an email to: cheminformatics-unsubscribe at yahoogroups.com Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service. K. R. Rupesh, Department of Biotechnology, Pondicherry University, Pondicherry-605014, India. 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