From nish.iitg at gmail.com Wed Jun 6 03:48:02 2007 From: nish.iitg at gmail.com (nisha rajagopal) Date: Wed, 6 Jun 2007 13:18:02 +0530 Subject: [BiO BB] high school project in bioinformatics Message-ID: <99789a220706060048s19155cabva57542ff1f05bd79@mail.gmail.com> Hi My sister is a student of class 12 and as part of her biology project she would like to work on an area in bioinformatics. I went through the suggestion given in one of the postings : "How about a protein sequence colorer? Read a FASTA file, and use different color schemes based on charge, hydrophobicity, size, polarity. This could also be turned into a simple hydropathy indexing plot, thus a primitive membrane protein predictor. If this sounds like an underkill, apply same idea to a multiple sequence alignment. Conservation indices etc. may be calculated for each column. " While my sister is good at Math and biology she does not know much of computer programming. Would this project be feasible for her? Could you also describe the project in more detail? Thanks, Nisha From lcharari at yahoo.com Wed Jun 6 06:13:32 2007 From: lcharari at yahoo.com (Daniel Harari) Date: Wed, 6 Jun 2007 03:13:32 -0700 (PDT) Subject: [BiO BB] Consensus Sequence Plots Message-ID: <20070606101332.37493.qmail@web51603.mail.re2.yahoo.com> Dear all, I am in need of a program that will have the capacity to scan large files of multiple sequence protein alignments (e.g 2500 sequences of a protein 500 amino acids in length), in the search regions of consensus sequences. The input alignment file will be in clustal or Muscle format. I am looking for either a graphical or tabular output, where if possible, it would be able to home in on regions of interest and analyze them more thoroughly. Any recommendations would be very much appreciated. Regards, Daniel Daniel Harari, PhD. Chaim Orbach 15A. Rehovot, 76534 ISRAEL Email: daniel.harari at yahoo.com Phone: +972-8-931-5943 Mobile: +972-544-241-168 --------------------------------- Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. From Diane.Hager at Colorado.EDU Wed Jun 6 15:29:03 2007 From: Diane.Hager at Colorado.EDU (Diane Marie Hager) Date: Wed, 6 Jun 2007 13:29:03 -0600 Subject: [BiO BB] Boxshaded file to continuously print? Message-ID: Hello. I would like to know if there is an interface (or third party developed product) written that allows Boxshade to produce a continuous alignment, not segmented into 256 characters or some other page limitation. Some of our protein alignments are 18 feet long when printed on a roll of paper. I have been pasting the Boxshade results into Cored Draw and aligning them as one continuous result. This process allows for too much error on my part so I am looking for an alternative that would eliminate this step. If you know of any one who has already tackled this issue or have any advice for me, I would certainly appreciate the information. Thank you, Diane Hager McHenry Lab University of Colorado 303 735-2193 From sbotond at gmail.com Wed Jun 6 17:06:30 2007 From: sbotond at gmail.com (Sipos Botond) Date: Wed, 6 Jun 2007 23:06:30 +0200 Subject: [BiO BB] Consensus Sequence Plots In-Reply-To: <20070606101332.37493.qmail@web51603.mail.re2.yahoo.com> References: <20070606101332.37493.qmail@web51603.mail.re2.yahoo.com> Message-ID: <80797a220706061406i44659fb3x7236d506645e7967@mail.gmail.com> Hello! I think sequence logos may be useful for this problem. http://weblogo.berkeley.edu/ Botond. On 6/6/07, Daniel Harari wrote: > > Dear all, > > I am in need of a program that will have the capacity to scan large files > of multiple sequence protein alignments ( e.g 2500 sequences of a protein > 500 amino acids in length), in the search regions of consensus > sequences. The input alignment file will be in clustal or Muscle > format. I am looking for either a graphical or tabular output, where if > possible, it would be able to home in on regions of interest and analyze > them more thoroughly. > > Any recommendations would be very much appreciated. > > Regards, > > Daniel > > > Daniel Harari, PhD. > Chaim Orbach 15A. > Rehovot, 76534 > ISRAEL > Email: daniel.harari at yahoo.com > Phone: +972-8-931-5943 > Mobile: +972-544-241-168 > > --------------------------------- > Boardwalk for $500? In 2007? Ha! > Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! > Games. > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From joypaul.joy at gmail.com Thu Jun 7 02:05:30 2007 From: joypaul.joy at gmail.com (Joy Paul) Date: Thu, 7 Jun 2007 11:35:30 +0530 Subject: [BiO BB] high school project in bioinformatics In-Reply-To: <99789a220706060048s19155cabva57542ff1f05bd79@mail.gmail.com> References: <99789a220706060048s19155cabva57542ff1f05bd79@mail.gmail.com> Message-ID: <33e5e0730706062305w51a8f1afv1b21db8dbab6ecf2@mail.gmail.com> dear nisha, firstly, the protein sequence colorer project is worthwhile and there are web applications which serves the same purpose and is the essence of bioinformatics. But, to make this on ur own would require some basic skills in programming, say c, c++ or even the more easier perl. for finding out the coloring based on physiochemical parameters , she would require the theory behind it or the the algorithm behind it. The theory is fairly easy to understand, but still have to read it closely. The multiple sequence alignment stuff is little advanced and u should consult a preliminary bioinformatics book for ur convenience.. All in all she should know some programming to implement these. otherwise, websites doing these jobs are present. U can always use these websites and get some or ur own ideas to extract something. http://www.expasy.ch/cgi-bin/protscale.pl http://www.bmm.icnet.uk/~offman01/hydro.html Joy Paul. On 6/6/07, nisha rajagopal wrote: > > Hi > > My sister is a student of class 12 and as part of her biology project > she would like to work on an area in bioinformatics. > I went through the suggestion given in one of the postings : > > "How about a protein sequence colorer? Read a FASTA file, and use > different color schemes based on charge, hydrophobicity, size, polarity. > This could also be turned into a simple hydropathy indexing plot, thus a > primitive membrane protein predictor. > If this sounds like an underkill, apply same idea to a multiple > sequence alignment. Conservation indices etc. may be calculated for > each column. " > While my sister is good at Math and biology she does not know much of > computer programming. > Would this project be feasible for her? Could you also describe the > project in more detail? > Thanks, > Nisha > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- joy paul. my karma ran over your dogma. From answer.dev at gmail.com Thu Jun 7 00:38:58 2007 From: answer.dev at gmail.com (DEV SINGH) Date: Thu, 7 Jun 2007 10:08:58 +0530 Subject: [BiO BB] high school project in bioinformatics In-Reply-To: <99789a220706060048s19155cabva57542ff1f05bd79@mail.gmail.com> References: <99789a220706060048s19155cabva57542ff1f05bd79@mail.gmail.com> Message-ID: <1708f1960706062138n64b414bhff80681bd0640348@mail.gmail.com> ok peoject & project idea both is good for 12th classs standard. plz see this link for online. EBI server for multiple sequence alignment on the web. www.ebi.ac.uk/*clustalw * *or u can install jalview software which is java supported ,& do the same sequence analysis.* *also take the help of matlab(software) tool box for bioinformatics* *u can do some mini project using link: http://au.expasy.org/tools/* ** ** On 6/6/07, nisha rajagopal wrote: > > Hi > > My sister is a student of class 12 and as part of her biology project > she would like to work on an area in bioinformatics. > I went through the suggestion given in one of the postings : > > "How about a protein sequence colorer? Read a FASTA file, and use > different color schemes based on charge, hydrophobicity, size, polarity. > This could also be turned into a simple hydropathy indexing plot, thus a > primitive membrane protein predictor. > If this sounds like an underkill, apply same idea to a multiple > sequence alignment. Conservation indices etc. may be calculated for > each column. " > While my sister is good at Math and biology she does not know much of > computer programming. > Would this project be feasible for her? Could you also describe the > project in more detail? > Thanks, > Nisha > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From lijo.skb at gmail.com Thu Jun 7 04:56:31 2007 From: lijo.skb at gmail.com (lijo skb) Date: Thu, 7 Jun 2007 14:26:31 +0530 Subject: [BiO BB] Consensus Sequence Plots In-Reply-To: <80797a220706061406i44659fb3x7236d506645e7967@mail.gmail.com> References: <20070606101332.37493.qmail@web51603.mail.re2.yahoo.com> <80797a220706061406i44659fb3x7236d506645e7967@mail.gmail.com> Message-ID: Y can't you seek help from www.sooryakiran.com, kiran.soorya at gmail.com. They are pretty good guys in assiting bioinformatcians. regards Li On 6/7/07, Sipos Botond wrote: > > Hello! > > I think sequence logos may be useful for this problem. > http://weblogo.berkeley.edu/ > > Botond. > > > > On 6/6/07, Daniel Harari wrote: > > > > Dear all, > > > > I am in need of a program that will have the capacity to scan large > files > > of multiple sequence protein alignments ( e.g 2500 sequences of a > protein > > 500 amino acids in length), in the search regions of consensus > > sequences. The input alignment file will be in clustal or Muscle > > format. I am looking for either a graphical or tabular > output, where if > > possible, it would be able to home in on regions of interest and analyze > > them more thoroughly. > > > > Any recommendations would be very much appreciated. > > > > Regards, > > > > Daniel > > > > > > Daniel Harari, PhD. > > Chaim Orbach 15A. > > Rehovot, 76534 > > ISRAEL > > Email: daniel.harari at yahoo.com > > Phone: +972-8-931-5943 > > Mobile: +972-544-241-168 > > > > --------------------------------- > > Boardwalk for $500? In 2007? Ha! > > Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! > > Games. > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Lijo From marchywka at hotmail.com Thu Jun 7 11:54:52 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 07 Jun 2007 11:54:52 -0400 Subject: [BiO BB] Consensus Sequence Plots In-Reply-To: Message-ID: I've written some scripts to parse and format clustalw output. For something that large you may want native code but, alternatively, if these really come from clustalw the source code is available so you can do whatever you want. I would point out, however, that you may need to be careful with specifics. I've tried getting clustal to align individual probes to a gene and had better luck, for my purposes, with simplistic no-gap code. Anytime you start using tools in different regions of parameter space it may be important to have ways to validate them. Scripts often work here as they can be quick to write but slow to execute- just what you want for validation but not production. In short- try cygwin or even debian. >From: "lijo skb" >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] Consensus Sequence Plots >Date: Thu, 7 Jun 2007 14:26:31 +0530 > >Y can't you seek help from www.sooryakiran.com, kiran.soorya at gmail.com. >They >are pretty good guys in assiting bioinformatcians. > >regards >Li > > >On 6/7/07, Sipos Botond wrote: >> >>Hello! >> >>I think sequence logos may be useful for this problem. >>http://weblogo.berkeley.edu/ >> >>Botond. >> >> >> >>On 6/6/07, Daniel Harari wrote: >> > >> > Dear all, >> > >> > I am in need of a program that will have the capacity to scan large >>files >> > of multiple sequence protein alignments ( e.g 2500 sequences of a >>protein >> > 500 amino acids in length), in the search regions of consensus >> > sequences. The input alignment file will be in clustal or Muscle >> > format. I am looking for either a graphical or tabular >>output, where if >> > possible, it would be able to home in on regions of interest and >>analyze >> > them more thoroughly. >> > >> > Any recommendations would be very much appreciated. >> > >> > Regards, >> > >> > Daniel >> > >> > >> > Daniel Harari, PhD. >> > Chaim Orbach 15A. >> > Rehovot, 76534 >> > ISRAEL >> > Email: daniel.harari at yahoo.com >> > Phone: +972-8-931-5943 >> > Mobile: +972-544-241-168 >> > >> > --------------------------------- >> > Boardwalk for $500? In 2007? Ha! >> > Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! >> > Games. >> > _______________________________________________ >> > General Forum at Bioinformatics.Org - >> > BiO_Bulletin_Board at bioinformatics.org >> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > >>_______________________________________________ >>General Forum at Bioinformatics.Org - >>BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > > >-- >Lijo >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm From marchywka at hotmail.com Thu Jun 7 12:03:23 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 07 Jun 2007 12:03:23 -0400 Subject: [BiO BB] high school project in bioinformatics In-Reply-To: <1708f1960706062138n64b414bhff80681bd0640348@mail.gmail.com> Message-ID: Rule number 1: Never pay for anything: Before you try matlab, give "R" a shot- free and IIRC has source code too. http://cran.cnr.berkeley.edu/ Clustalw source code is free and it builds under cygwin ( I just did this myself). If you are just learning and go with the coloring idea, try this whey you get cygwin running: 506 lynx -dump "http://www.expasy.org/cgi-bin/protscale.pl?Q7U3V6" > plinks 507 cat plinks | grep pscale | awk '{print $2}' > links 508 more links 509 for f in `cat links`; do echo $f ; done 510 for f in `cat links|head -n 1`; do lynx -dump "$f" ; done 516 for f in `cat links`; do echo "$f"; lynx -dump "$f"| grep "scale:\|^[A-Z][a-z][a-z]:" ; done >extracted_scales Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com _________________________________________________________________ Get a preview of Live Earth, the hottest event this summer - only on MSN http://liveearth.msn.com?source=msntaglineliveearthhm From codeshepherd at gmail.com Sat Jun 9 03:40:55 2007 From: codeshepherd at gmail.com (=?ISO-8859-1?Q?D=EB=EA=FE=E0=F1_=C7h=E4kr=E3v=E2rth=FF?=) Date: Sat, 09 Jun 2007 15:40:55 +0800 Subject: [BiO BB] high school project in bioinformatics In-Reply-To: <99789a220706060048s19155cabva57542ff1f05bd79@mail.gmail.com> References: <99789a220706060048s19155cabva57542ff1f05bd79@mail.gmail.com> Message-ID: <466A5987.5070303@gmail.com> nisha rajagopal wrote: > Hi > > My sister is a student of class 12 and as part of her biology project > she would like to work on an area in bioinformatics. > I went through the suggestion given in one of the postings : > > "How about a protein sequence colorer? Read a FASTA file, and use > different color schemes based on charge, hydrophobicity, size, polarity. > This could also be turned into a simple hydropathy indexing plot, thus a > primitive membrane protein predictor. > If this sounds like an underkill, apply same idea to a multiple > sequence alignment. Conservation indices etc. may be calculated for > each column. " > While my sister is good at Math and biology she does not know much of > computer programming. > Would this project be feasible for her? Could you also describe the > project in more detail? > Thanks, > Nisha Hi Nisha, Most protein visualizers can do what you are trying to do. If she is not an expert in programming, I would suggest her to pick up some existing tools and work on them. Taverna is a very good work flow system. Its is a opensource software. there are many such tools available. I just quoted taverna because it is in the recent hit list. First find out what her interests are and try out to come with an idea. Once you have an idea, you can post your idea here and ask people for the suitable tools available to achieve the target. Thanks Deepan http://codeshepherd.com/ > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From rick.casey at colorado.edu Tue Jun 12 11:51:43 2007 From: rick.casey at colorado.edu (Rick Casey) Date: Tue, 12 Jun 2007 09:51:43 -0600 Subject: [BiO BB] Plone and bioinformatics? Message-ID: <466EC10F.1020308@colorado.edu> I am new to this site, so have not had any experience here yet; but wanted to ask this community a question. I work at the Institute for Behavioral Genetics in Boulder (ibgwww.colorado.edu), where I am constructing an inhouse, web-based database to serve as a central repository for their research data and analysis. I've been working on this for about two and half years now, using PostGres as the backend database, and PHP for the web interface, with some occasional Perl. Progress has been steady but slow, and I am searching for better software development tools to use on this project. I would like to ask if anyone here has experience using Plone? It seems to be a leading candidate for the kind of tool I need. Where this project gets bogged down is developing webpages that communicate with the database, and in using a relational schema. It would seem that an object-oriented schema would be better for the complex data structures required in a genetics laboratory environment. Making schema changes to a relational structure, and then modifying PHP code tied to it, is quite labor intensive. I am hoping that an O-O schema plus using a content management system will help with this; but would like to "look before I leap", so to speak. So if anyone has experience relevant to this type of development, I would like to hear about it. I would also be willing to share more details about our project, if anyone should be interested. Best regards, Rick Casey rick.casey at colorado.edu Professional Research Assistant Institute for Behavioral Genetics University of Colorado at Boulder From marchywka at hotmail.com Wed Jun 13 16:52:20 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 13 Jun 2007 16:52:20 -0400 Subject: [BiO BB] Plone and bioinformatics? In-Reply-To: <466EC10F.1020308@colorado.edu> Message-ID: Knowing absolutely nothing about your objectives, I will assume they are similar to mine :) That is, they want a database to facilitate research and data mining. First, these guys seem to have gotten just about everything right: http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html and claim to have tools available ( mostly c++ code for their apps but they maintain a bunch of gene/protein sequence databases and even expression array data). Second, my own personal comment, don't worry about a web interface as much as an API and put the graphics stuff on top of that. Any "serious" work almost always requires working around the gui. If they have any public stuff or even internal use equivalntes- like an epitope database or gene expression array data or specialized servers ( upload a sequence, get an analysis back) just make the data available with an API and let the specialized users write the code to implement their one-off ideas. Many people think the graphics ARE the science- obviously I don't work for Microsoft :) In short, I am essentially advocating that you write some terse code to make a GENERAL, user-sensible query into SQL for postgres. Check boxes, common queries, trying to out guess the serious user is essentially impossible but you always need common pages for the casual user, users testing scripts, and demonstrations. Obviously, if your sponsor has a different idea it may take some selling but I think the end-product would be more usable and even more maintainable ( don't try to design an interface or database around a gui). Even if they have just one "thing" they want everyone to do, you can write a simple web page for that and have the other stuff ready when they change their mind. So, I guess my response is store the data in the most flexible possible way and make general programmatic access availabe in an API and don't worry about clever stuff- that's for researchers not web page designers. Having an "output as text" option for everything, including spatial data that can be reduced to vectors or something, is a big help. >From: Rick Casey >Reply-To: "General Forum at Bioinformatics.Org" > >To: bbb at bioinformatics.org >Subject: [BiO BB] Plone and bioinformatics? >Date: Tue, 12 Jun 2007 09:51:43 -0600 > >I am new to this site, so have not had any experience here yet; but wanted >to ask this community a question. > >I work at the Institute for Behavioral Genetics in Boulder >(ibgwww.colorado.edu), where I am constructing an inhouse, web-based >database to serve as a central repository for their research data and >analysis. > >I've been working on this for about two and half years now, using PostGres >as the backend database, and PHP for the web interface, with some >occasional Perl. Progress has been steady but slow, and I am searching for >better software development tools to use on this project. > >I would like to ask if anyone here has experience using Plone? It seems to >be a leading candidate for the kind of tool I need. Where this project gets >bogged down is developing webpages that communicate with the database, and >in using a relational schema. > >It would seem that an object-oriented schema would be better for the >complex data structures required in a genetics laboratory environment. >Making schema changes to a relational structure, and then modifying PHP >code tied to it, is quite labor intensive. I am hoping that an O-O schema >plus using a content management system will help with this; but would like >to "look before I leap", so to speak. > >So if anyone has experience relevant to this type of development, I would >like to hear about it. I would also be willing to share more details about >our project, if anyone should be interested. > >Best regards, >Rick Casey >rick.casey at colorado.edu >Professional Research Assistant >Institute for Behavioral Genetics >University of Colorado at Boulder > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ PC Magazine?s 2007 editors? choice for best Web mail?award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HM_mini_pcmag_0507 From bioinfosm at gmail.com Wed Jun 13 16:48:27 2007 From: bioinfosm at gmail.com (Samantha Fox) Date: Wed, 13 Jun 2007 16:48:27 -0400 Subject: [BiO BB] Phylip distance matrix symmetry error Message-ID: <726450810706131348s7ce2c7bcpd113ee50b575d80d@mail.gmail.com> ERROR: distance matrix is not symmetric: (42,1) element and (1,42) element are unequal. They are 1.544868 and 1.544868, respectively. Is it a distance matrix? That looks symmetric to me !! Any clues anyone ?? ~S From lijo.skb at gmail.com Thu Jun 14 00:26:23 2007 From: lijo.skb at gmail.com (lijo skb) Date: Thu, 14 Jun 2007 09:56:23 +0530 Subject: [BiO BB] Plone and bioinformatics? In-Reply-To: References: <466EC10F.1020308@colorado.edu> Message-ID: Dear Rick Casey, I suggest another team, exuberant young researchers group namely soorkiran bioiformatics . Perhaps we could help you to successful execution of you project. Warm regards Lijo On 6/14/07, Mike Marchywka wrote: > > Knowing absolutely nothing about your objectives, I will assume they > are similar to mine :) > That is, they want a database to facilitate research and data mining. > First, these guys seem to have gotten just about everything right: > > http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html > > and claim to have tools available ( mostly c++ code for their apps > but they maintain a bunch of gene/protein sequence databases and > even expression array data). > > Second, my own personal comment, don't worry about a web interface > as much as an API and put the graphics stuff on top of that. Any "serious" > work almost always requires working around the gui. If they have > any public stuff or even internal use equivalntes- > like an epitope database or gene expression array data or > specialized servers ( upload a sequence, get an analysis back) just > make the data available with an API and let the specialized users write > the > code to implement their one-off ideas. Many people think > the graphics ARE the science- obviously I don't work for Microsoft :) > > In short, I am essentially advocating that you write some terse code to > make a GENERAL, user-sensible query into SQL for postgres. Check boxes, > common queries, > trying to out guess the serious user is essentially impossible but you > always need > common pages for the casual user, users testing scripts, and > demonstrations. > Obviously, if your > sponsor has a different idea it may take some selling but I think the > end-product > would be more usable and even more maintainable ( don't try to design > an interface or database around a gui). Even if they have just one "thing" > they want > everyone to do, you can write a simple web page for that and have the > other stuff ready when they change their mind. > > > So, I guess my response is store the data in the most flexible possible > way > and make > general programmatic access availabe in an API and don't worry about > clever > stuff- > that's for researchers not web page designers. Having an "output as text" > option > for everything, including spatial data that can be reduced to vectors or > something, > is a big help. > > > > > > > > >From: Rick Casey > >Reply-To: "General Forum at Bioinformatics.Org" > > > >To: bbb at bioinformatics.org > >Subject: [BiO BB] Plone and bioinformatics? > >Date: Tue, 12 Jun 2007 09:51:43 -0600 > > > >I am new to this site, so have not had any experience here yet; but > wanted > >to ask this community a question. > > > >I work at the Institute for Behavioral Genetics in Boulder > >(ibgwww.colorado.edu), where I am constructing an inhouse, web-based > >database to serve as a central repository for their research data and > >analysis. > > > >I've been working on this for about two and half years now, using > PostGres > >as the backend database, and PHP for the web interface, with some > >occasional Perl. Progress has been steady but slow, and I am searching > for > >better software development tools to use on this project. > > > >I would like to ask if anyone here has experience using Plone? It seems > to > >be a leading candidate for the kind of tool I need. Where this project > gets > >bogged down is developing webpages that communicate with the database, > and > >in using a relational schema. > > > >It would seem that an object-oriented schema would be better for the > >complex data structures required in a genetics laboratory environment. > >Making schema changes to a relational structure, and then modifying PHP > >code tied to it, is quite labor intensive. I am hoping that an O-O schema > >plus using a content management system will help with this; but would > like > >to "look before I leap", so to speak. > > > >So if anyone has experience relevant to this type of development, I would > >like to hear about it. I would also be willing to share more details > about > >our project, if anyone should be interested. > > > >Best regards, > >Rick Casey > >rick.casey at colorado.edu > >Professional Research Assistant > >Institute for Behavioral Genetics > >University of Colorado at Boulder > > > >_______________________________________________ > >General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _________________________________________________________________ > PC Magazine's 2007 editors' choice for best Web mail?award-winning Windows > Live Hotmail. > > http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HM_mini_pcmag_0507 > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Lijo From marchywka at hotmail.com Thu Jun 14 12:36:25 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 14 Jun 2007 12:36:25 -0400 Subject: [BiO BB] Phylip distance matrix symmetry error In-Reply-To: <726450810706131348s7ce2c7bcpd113ee50b575d80d@mail.gmail.com> Message-ID: As they told me in junior high programming, NEVER make a floating point equality compare ( zero may be ok, but that is questionable) :): (epsilon^2From: "Samantha Fox" >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: [BiO BB] Phylip distance matrix symmetry error >Date: Wed, 13 Jun 2007 16:48:27 -0400 > >ERROR: distance matrix is not symmetric: > (42,1) element and (1,42) element are unequal. > They are 1.544868 and 1.544868, respectively. > Is it a distance matrix? > >That looks symmetric to me !! >Any clues anyone ?? > >~S >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Like puzzles? Play free games & earn great prizes. Play Clink now. http://club.live.com/clink.aspx?icid=clink_hotmailtextlink2 From jeff at bioinformatics.org Thu Jun 14 13:59:54 2007 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 14 Jun 2007 13:59:54 -0400 Subject: [BiO BB] Plone and bioinformatics? In-Reply-To: References: <466EC10F.1020308@colorado.edu> Message-ID: <4671821A.4040005@bioinformatics.org> lijo skb wrote: > > I suggest another team, exuberant young researchers group namely > ... <...>. Perhaps we could help you to > successful execution of you project. Please see the list's information page for what is appropriate to post: https://bioinformatics.org/mailman/listinfo/bio_bulletin_board While it's sometimes necessary to post a link to a for-profit website (if, for example, they provide the only solution to a problem), the above post is generic and simply spam. It's also the second time (7 days ago) that Lijo did this. We apologize that this made it through. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From logan at cacs.louisiana.edu Fri Jun 15 19:33:08 2007 From: logan at cacs.louisiana.edu (Raja Loganantharaj) Date: Fri, 15 Jun 2007 18:33:08 -0500 Subject: [BiO BB] Blast tree view widget Message-ID: <467321B4.6010502@cacs.louisiana.edu> NCBI has a cool program to display sequence pairwise distances over the WEB. Does anyone know how to get a copy of the widget or how they do it. I guess the input to the widget is a 2x2 distance matrix. Pointer to any other similar program to display nodes using the distance is appreciated. Googling did not help. Thanks From marchywka at hotmail.com Fri Jun 15 20:31:49 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 15 Jun 2007 20:31:49 -0400 Subject: [BiO BB] Blast tree view widget In-Reply-To: <467321B4.6010502@cacs.louisiana.edu> Message-ID: Did you try asking them? Their general help desk could probably get you to developers but they probably have a link somewhere. I've never had a problem getting info from them on just about anything. As far as google, try something with the term "visualization" as in "data visualization" for a start. The clustering search engines always help get me started, try vivisimo or clusty ( can't remember which name is more recent). FWIW, I went crazy with openGL for molecule viewing ( not all the features of RasMol yet, but almost as fast in some modes and nice for custom code trials like cavity fill- I have some artistic interaction surfaces [ still looking for realistic potentials ]) and started to add a general purpose graphing system. This is kluged right now but amazingly easy to write. My point is that if you have a c++ compiler you can probably write your own pretty quickly. Don't underestimate how quickly templatized OO code lets you build up a resuable code library either and also don't forget how easy it is to write a one page program that you can pipe to and from. I have had some experimental distance measures and I could write them in a page of code and tack them onto a "main" method- then I have something that works with all my scripts. There are always a few caveats for performance - I ripped out all the ">>" junk for reading fasta files in favor of "readsome" ( or whatever the method is for buffer access, I'm away from the code right now)- but usually you don't have to track down flakely memory corruption problems etc. If you want to move slowly, main(argc argv) works just as a class method as it does at global scope :) >From: Raja Loganantharaj >Reply-To: logan at cacs.louisiana.edu,"General Forum at Bioinformatics.Org" > >To: "The general forum at Bioinformatics.Org" > >Subject: [BiO BB] Blast tree view widget >Date: Fri, 15 Jun 2007 18:33:08 -0500 > >NCBI has a cool program to display sequence pairwise distances over the >WEB. Does anyone know how to get a copy of the widget or how they do it. I >guess the input to the widget is a 2x2 distance matrix. Pointer to any >other similar program to display nodes using the distance is appreciated. >Googling did not help. > >Thanks > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Don?t miss your chance to WIN $10,000 and other great prizes from Microsoft Office Live http://clk.atdmt.com/MRT/go/aub0540003042mrt/direct/01/ From smagarwal at yahoo.com Sat Jun 16 01:25:03 2007 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Sat, 16 Jun 2007 06:25:03 +0100 (BST) Subject: [BiO BB] PFAM Message-ID: <208738.76398.qm@web31501.mail.mud.yahoo.com> Hi all Can anyone let me know that how the seed sequences are selected in PFAM. Thanks Subhash The DELETE button on Yahoo! Mail is unhappy. Go here to know why- http://in.mail.yahoo.com From brij at silicogene.com Sat Jun 16 02:51:59 2007 From: brij at silicogene.com (Life-Science Search Engine) Date: Sat, 16 Jun 2007 12:21:59 +0530 Subject: [BiO BB] Customized Life-Science Search Engine Message-ID: Hi, The link below is a Google Sponsored Customized search for Life sciences related research. It is foccused and very effective for all those working in Life Science and related activities. Above all it is from Google and free!! The link is : http://www.brij.in/ From pfern at igc.gulbenkian.pt Sat Jun 16 10:53:29 2007 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Sat, 16 Jun 2007 15:53:29 +0100 Subject: [BiO BB] Phylip distance matrix symmetry error In-Reply-To: <726450810706131348s7ce2c7bcpd113ee50b575d80d@mail.gmail.com> References: <726450810706131348s7ce2c7bcpd113ee50b575d80d@mail.gmail.com> Message-ID: <1182005609.4673f969eee01@webmail.igc.gulbenkian.pt> Hi Samantha I may be missing the ccontext... but: 1) There may be a precision problem, any real number in a computer is rich in decimal places that are not always seen, what is displayed is less precise, so: subtract the numbers! 2) Some (!) Phylip rograms are known to be sensitive to invisible stuff on input (insvisible being spaces, tabs, etc. So you may be evaluating somenthing that is read with a wrong format. 3) Check carefully the origin and contents of all your files. Use Notepad++ for example. Good luck Pedro -- Pedro Fernandes Centro Portugu?s de Bioinform?tica Instituto Gulbenkian de Ci?ncia Apartado 14 2781 OEIRAS PORTUGAL ----------------------------------------------------------- CONFIDENCIAL. Esta mensagem e os ficheiros eventualmente anexos s?o confidenciais. Se tiver recebido esta mensagem por engano, agradecemos que nos contacte imediatamente por e-mail ou pelo telefone +351 21 4407912 e que elimine a mensagem e ficheiros anexos sem os reproduzir. Quoting Samantha Fox : > ERROR: distance matrix is not symmetric: > (42,1) element and (1,42) element are unequal. > They are 1.544868 and 1.544868, respectively. > Is it a distance matrix? > > That looks symmetric to me !! > Any clues anyone ?? > > ~S > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From marchywka at hotmail.com Mon Jun 18 19:20:33 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 18 Jun 2007 19:20:33 -0400 Subject: [BiO BB] Phylip distance matrix symmetry error In-Reply-To: <1182005609.4673f969eee01@webmail.igc.gulbenkian.pt> Message-ID: Was this posted here already? http://www.the-scientist.com/news/home/53289/ Just a reminder to check your stuff for consistency at every step:) The problem you describe, however, should either generate a WARNING or have an interface that doesn't request redundant values. Hacking up a nice regular array can be cumbersome so it is probably easier to send duplicate values. The code may make use of assumed relationships but you would think the more naive brute force code would be available if constraints are violated. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com >From: Pedro Fernandes >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] Phylip distance matrix symmetry error >Date: Sat, 16 Jun 2007 15:53:29 +0100 > >Hi Samantha > >I may be missing the ccontext... but: > >1) There may be a precision problem, any real number in a computer is rich >in >decimal places that are not always seen, what is displayed is less precise, >so: >subtract the numbers! > >2) Some (!) Phylip rograms are known to be sensitive to invisible stuff on >input >(insvisible being spaces, tabs, etc. So you may be evaluating somenthing >that is >read with a wrong format. > >3) Check carefully the origin and contents of all your files. Use Notepad++ >for >example. > >Good luck >Pedro > >-- >Pedro Fernandes >Centro Portugu??s de Bioinform??tica >Instituto Gulbenkian de Ci??ncia >Apartado 14 >2781 OEIRAS >PORTUGAL >----------------------------------------------------------- >CONFIDENCIAL. Esta mensagem e os ficheiros eventualmente anexos s??o >confidenciais. Se tiver recebido esta mensagem por engano, agradecemos >que nos contacte imediatamente por e-mail ou pelo telefone +351 21 4407912 >e que elimine a mensagem e ficheiros anexos sem os reproduzir. > > > >Quoting Samantha Fox : > > > ERROR: distance matrix is not symmetric: > > (42,1) element and (1,42) element are unequal. > > They are 1.544868 and 1.544868, respectively. > > Is it a distance matrix? > > > > That looks symmetric to me !! > > Any clues anyone ?? > > > > ~S > > _______________________________________________ > > General Forum at Bioinformatics.Org - >BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Picture this ? share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHM&loc=us From asidhu at biomap.org Mon Jun 18 16:32:37 2007 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Tue, 19 Jun 2007 06:32:37 +1000 Subject: [BiO BB] CFP: 2007 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2007) Message-ID: <1182198757.4676ebe555ac4@mail.opentransfer.com> 2007 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2007) (co-located with IEEE/WCI/ACM WI-IAT 07 and IEEE GrC 07) http://www.cis.drexel.edu/faculty/thu/bibm/index.php.htm San Jose, CA, USA Nov 2-4, 2007 IEEE BIBM 2007 will provide a general forum for disseminating the latest research in bioinformatics and biomedicine. It is a multidisciplinary conference that brings together academic and industrial scientists from computer science, biology, chemistry, medicine, mathematics and statistics. It will exchange research results and address open issues in all aspects of bioinformatics and biomedicine and provide a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, simulation, ontology and other computational methods, as applied to life science problems, with emphasis on applications in high throughput data-rich areas in biology, biomedical engineering. IEEE BIBM 2007 intends to attract a balanced combination of computer scientists, biologists, biomedical engineers, chemist, data analyzer, statistician. Topics of interests We are soliciting high quality original research papers (including significant works-in-progress) in any aspect of bioinformatics and biomedicine. New computational techniques and methods in machine learning; data mining; text analysis; pattern recognition; knowledge representation; databases; data modeling; combinatorics; stochastic modeling; string and graph algorithms; linguistic methods; robotics; constraint satisfaction; data visualization; parallel computation; data integration; modeling and simulation and heir application in life science domain are especially encouraged. Relevant topics included, but are not limited to: ? Biological Data Mining ? High Performance Bio-computing ? Genomics, Comparative Genomics ? Biological Databases & Data Integration ? Biological Data Visualization ? Evolution and Phylogeny ? Molecular sequence analysis ? Healthcare Informatics ? Recognition of genes and regulatory elements ? Molecular evolution ? Proteomics, Protein structure, Computational proteomics ? Gene networks, Computational genetics ? Combinatorial libraries and drug design ? Computational systems biology ? Microarray design and data analysis ? BioOntologies ? Sequence Analysis ? Structural and functional genomics ? Synthetic Biological Systems ? Pathways, Networks , Systems Biology ? Text Mining & Information Extraction ? Transcriptomics ? BioMedical Devices with Embedded Computers ? Signal and Image Processing in BioMedicine ? BioMedical Image Segmentation and Compression ? BioMedical Intelligence and Data Warehousing ? BioMedical Databases & Information Systems , BioMedical Information ? Multimedia Biomedical Databases ? Intelligent Biomedical Knowledge Discovery ? Modeling signalling network ? Temporal and spatial mining of clinic data including medical images MEETING ORGANIZATION: GENERAL CO-CHAIRS: Prof. Yi Pan Department of Computer Science Georgia State University 34 Peachtree Street, Suite 1450 Atlanta, GA 30302-4110, USA Prof. Carmelina Ruggiero Editor-in-chief of IEEE Trans. on NanoBioscience Professor of Bioengineering DIST University of Genoa Via Opera Pia 13 Genoa, 16145, Italy Prof. Aydin Tozeren Distinguished Professor and Director, Center for Integrated Bioinformatics, School of Biomedical Engineering, Science & Health Systems Drexel University, Philadelphia, PA 19104, USA PROGRAM CO-CHAIRS: Prof. Xiaohua Hu College of Information Science & Technology Drexel University Philadelphia, PA 19104 USA Prof. Zoran Obradovic Center for Information Science and Technology, Temple University, 303 Wachman Hall (038-24), 1805 N. Broad St., Philadelphia, PA 19122, USA. Prof. Ion Mandoiu Computer Science & Engineering Department University of Connecticut 371 Fairfield Way, Unit 2155 Storrs, CT 06269-2155 Office: ITEB 261 WORKSHOP CHAIRS: Jinyan Li Institute for Infocomm Research, Singapore Xue-Wen Chen Univ. of Kansas, USA Tharam S. Dillon Curtin University of Technology, Australia TUTORIAL CHAIR: Sun Kim Indiana University, USA LOCAL ACCOMMODATION CO-CHAIRS: David Scot Taylor San Jos? State University, USA Tom Qi Zhang Google, USA PUBLICITY CO-CHAIRS: Amandeep S. Sidhu Curtin University of Technology, Australia Shuigeng Zhou Fudan University, China IEEE BIBM CO-CHAIRS/DIRECTORS: Xiaohua Hu Drexel University, USA Yi Pan Georgia State University, USA IEEE BIBM STEERING COMMITTEE: Xiaohua Hu Drexel University, USA Vipin Kumar Univ. of Minnesota, USA Michael Ng HongKong Baptist University, China Zoran Obradovic Temple University, USA Yi Pan Georgia State University, USA Jose Principe Univ. of Florida, USA Carmelina Ruggiero DIST University of Genoa, Italy Niilo Saranummi VTT Information Technology, Finland Shusaku Tsumoto Shimane University, Japan SUBMISSION REQUIREMENTS: Please submit a full length paper (not exceeding 5000 words) thorough the online submission system (The paper format is very flexible, if you prefer to prepare your paper in IEEE 2-column format, you can download the format instruction here for Latex or word). Electronic submissions (in PDF or Postscript format) are required. Accepted papers will be published in the conference proceedings by the IEEE Computer Society Press that are indexed by EI. The Best papers selected from the IEEE BIBM 07 will be published as a special issue in related IEEE Transactions and other journals such as IJDMB, IJBRA etc. IMPORTANT DATES: Paper submission: June 30, 2007 Notification: August 1, 2007 Camera-ready due: August 20, 2007 From christoph.gille at charite.de Tue Jun 19 15:10:24 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue, 19 Jun 2007 21:10:24 +0200 (CEST) Subject: [BiO BB] fortran intel macintosh Message-ID: <40463.141.42.56.114.1182280224.squirrel@webmail.charite.de> Hi All, I need an Intel Mac user who could compile a fortran and a C program for me. Thanks Christoph From codeshepherd at gmail.com Tue Jun 19 23:51:57 2007 From: codeshepherd at gmail.com (=?ISO-8859-1?Q?D=EB=EA=FE=E0=F1_=C7h=E4kr=E3v=E2rth=FF?=) Date: Wed, 20 Jun 2007 11:51:57 +0800 Subject: [BiO BB] fortran intel macintosh In-Reply-To: <40463.141.42.56.114.1182280224.squirrel@webmail.charite.de> References: <40463.141.42.56.114.1182280224.squirrel@webmail.charite.de> Message-ID: <4678A45D.9000009@gmail.com> Dr. Christoph Gille wrote: > Hi All, > I need an Intel Mac user who could compile > a fortran and a C program for me. > > Thanks > > Christoph > > Hi Christoph, Contact me offline, or try #mac #macosx @irc.freenode.net. Thanks Deepan From marchywka at hotmail.com Tue Jun 26 09:55:55 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 26 Jun 2007 09:55:55 -0400 Subject: [BiO BB] Affymetrix probe annotation- anyone need to identify unknowns? Message-ID: Hi, I've developed a bunch of scripts specifically to track down speculative annotations for unknown probe ID's from the Affymetrix canine array. I've turned up a bunch of interesting things that compare favorably to the annotations in their download files and web pages. If anyone has any interest in evaluating the quality of these assignments or knows of better approaches I'd be happy to learn about them or run a few probe ID's and share my recent results and interact. My process requires a list of probe ID's that I can first run against their latest annotation download file. For those with unsatisfactory annotations, I run a more complicated blast search ( typically taking about 1 hour per probe set ) and a second script for pulling out most reasonable matches. Personally I think I've found some very interesting results but could obviously use more expert commentary and criticism. It is now completely automated- give it a probe list, invoke 2 scripts, and get back a hit list. But, it is specialized to canine data just due to the Affymetrix files I have ( I need to known which annotation file to parse and which web page to hit - both of these are hardcoded for dogs right now). The results include names and numbers of most likely suspects, clustalw ouput for these suspects, and lots of "raw data" including blast results, candidate fasta files, etc. The blast search part in the first script I have reasonable confidence for but the second part, automated hit extraction, is a lot more tentative. Please reply either on or off list as you see fit. Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com _________________________________________________________________ Picture this ? share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHM&loc=us From marchywka at hotmail.com Wed Jun 27 10:05:32 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 27 Jun 2007 10:05:32 -0400 Subject: [BiO BB] Affymetrix probe annotation- anyone need to identifyunknowns? In-Reply-To: Message-ID: As an example related to my earlier post, AFFX has this as a class R with little info https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=CANINE%3A1606074_AT (free,but need to register) with the reference to this: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucest&id=20431335 The automated scripts found these related things- I also have ORF comparisons but am just looking at gene/transcript alignments for now. $ cat likely_hits /cygdrive/e/new/temp/canis/dcm/1606074/temp AY656737.1- Canis familiaris isolate 1 breed Basenji mitochondrion, complete AY656738.1- Canis familiaris isolate 1 breed Jack Russell Terrier AY656739.1- Canis familiaris isolate 1 breed Poodle mitochondrion, complete AY656740.1- Canis familiaris isolate 1 breed Kerry Blue Terrier mitochondrion, AY656741.1- Canis familiaris isolate 1 breed Irish Setter mitochondrion, AY656742.1- Canis familiaris isolate 1 breed Old English Sheepdog AY656743.1- Canis familiaris isolate 1 breed Saint Bernard mitochondrion, AY656744.1- Canis familiaris isolate 1 breed English Springer Spaniel AY656745.1- Canis familiaris isolate 2 breed English Springer Spaniel Complete sequence is usually a spurious hit but in this case the entry could mean something: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=12700659 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=50301805 And the alignment is quite good ( I haven't checked orf's yet but I now generate these along with clustalw output for putative matches). ( obviously a proportional space font, like most graphics, makes a mess of the information...) CLUSTAL W (1.83) multiple sequence alignment CANINE_1606074_AT --------------------------------------------------------ACGC AY012152 AGGTTTGGTCCTAGCCTTCCTATTAGTTTTTAGTAGACTTACACATGCAAGCCTCCACGC **** CANINE_1606074_AT CCCAGTGAGAATGCCCTTAAAATCACCAGTGATCTAAAGGAGCAGGTATCAAGCACACTC AY012152 CCCAGTGAGAATGCCCTTAAAATCACCAGTGATCTAAAGGAGCAGGTATCAAGCACACTC ************************************************************ CANINE_1606074_AT TTAAGTAGCTCATAACACCTTGCTAAGCCACACCCCCACGGGATACAGCAGTGATAAAAA AY012152 TTAAGTAGCTCATAACACCTTGCTAAGCCACACCCCCACGGGATACAGCAGTGATAAAAA ************************************************************ CANINE_1606074_AT TTAAGCCATAAACGAAAGTTTGACTAAGCCATACTAAATAGGGTTGGTAAATTTCGTGCC AY012152 TTAAGCCATAAACGAAAGTTTGACTAAGCCATACTAAATAGGGTTGGTAAATTTCGTGCC ************************************************************ CANINE_1606074_AT AGCCACCGCGGTCATACGATTAACCCAAACTAATAGGCCTACGGCGTAAAGCGTGTTCAA AY012152 AGCCACCGCGGTCATACGATTAACCCAAACTAATAGGCCTACGGCGTAAAGCGTGTTCAA ************************************************************ CANINE_1606074_AT GATACTTTTACACTAAAGTTAAAACTTAACTAAGCCGTAAAAAGCTACAGTTATCATAAA AY012152 GATACTTTAACACTAAAGTTAAAACTTAACTAAGCCGTAAAAAGCTACAGTTATCATAAA ******** *************************************************** CANINE_1606074_AT ATAAACCACGAAAGTGACTTTATAATAATCTGACTACACGATAGCTAAGACCCAAACTGG AY012152 ATAAACCACGAAAGTGACTTTATAATAATCTGACTACACGATAGCTAAGACCCAAACTGG ************************************************************ CANINE_1606074_AT GATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTACAACAAAATAATTCG AY012152 GATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTACAACAAAATAATTCG ************************************************************ CANINE_1606074_AT CCAGAGGACTACTAGCAATAGCTTAAAACTCAAAGGGACTTGGCGGTGCTTTATATCCCT AY012152 CCAGGGGACTACTAGCAATAGCTTAAAACTCAAAGG-ACTTGGCGGTGCTTTATATCCCT **** ******************************* *********************** CANINE_1606074_AT CTAG-------------------------------------------------------- AY012152 CTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTCACCACCTTTCGCTAATT **** [ trailer tuncated] So, if anyone is interested in looking for better id's or could suggest a better source for annotations or suggest a reason why these hits are irrelevant, please contact me. It does appear that additional information is available beyond that posted on Affx site, at least for the canine array. Thanks. _________________________________________________________________ Need a break? Find your escape route with Live Search Maps. http://maps.live.com/default.aspx?ss=Restaurants~Hotels~Amusement%20Park&cp=33.832922~-117.915659&style=r&lvl=13&tilt=-90&dir=0&alt=-1000&scene=1118863&encType=1&FORM=MGAC01 From yvan.strahm at gmail.com Fri Jun 22 02:30:10 2007 From: yvan.strahm at gmail.com (yvan.strahm at gmail.com) Date: Thu, 21 Jun 2007 23:30:10 -0700 Subject: [BiO BB] A Bioperl module for dbEST report format Message-ID: <467B6C72.2080008@gmail.com> Hello, Does someone knows if Bioperl has a module to read the report format from dbEST (ftp://ftp.ncbi.nih.gov/repository/dbEST/)? Or one should write its own? here is an entry: IDENTIFIERS dbEST Id: 5 EST name: EST00006 GenBank Acc: M61958 GenBank gi: 272208 GDB Dsegment: D0S2525E CLONE INFO Clone Id: HHCSB86 Source: ATCC Id in host: 77063 DNA type: cDNA PRIMERS Sequencing: M13 Forward PolyA Tail: Unknown SEQUENCE TGCACAACCAAGTTTTGTGACTACGGGAAGGCTCCCGGGGCAGAGGAGTACGCTCAACAA GATGTGTTAAAGAAATCTTACTCCAAGGCCTTCACGCTGACCATCTCTGCCCTCTTTGTG ACACCCAAGACGACTGGGGCCCNGGTGGAGTTAAGCGAGCAGCAACTNCAGTTGTNGCCG AGTGATGTGGACAAGCTGTCACCCACTGACA Entry Created: May 26 1992 Last Updated: May 26 1992 PUTATIVE ID Assigned by submitter 2',3'-cyclic nucleotide phoshodiesterase LIBRARY dbEST lib id: 4 Lib Name: Hippocampus, Stratagene (cat. #936205) Organism: Homo sapiens Vector: lambdaZAP-II Description: Female, 2 years; oligo-dT + random primed cDNA synthesis; lambdaZAP-II vector, 1.0kb average insert size. SUBMITTER Name: Kerlavage, AR Lab: Bioinformatics Institution: The Institute for Genomic Research Address: 9712 Medical Center Drive, Rockville, MD 20850 USA Tel: 3018699056 Fax: 3018699423 E-mail: arkerlav at tigr.org CITATIONS PubMed ID: 2047873 Title: Complementary DNA sequencing: expressed sequence tags and human genome project Authors: Adams,M.D., Kelley,J.M., Gocayne,J.D., Dubnick,M., Polymeropoulos,M.H., Xiao,H., Merril,C.R., Wu,A., Olde,B., Moreno,R.F., etal Citation: Science 252: 1651-1656 1991 PubMed ID: 8401586 Title: Chromosomal distribution of 320 genes from a brain cDNA library Authors: Polymeropoulos,M.H., Xiao,H., Sikela,J.M., Adams,M., Venter,J.C., Merrill,C.R. Citation: Nat. Genet. 4: 381-386 1993 MAP DATA Map: 17 Method: Somatic Cell Hybridization: Polymeropoulos Citation: Polymeropoulos,M.H. 1993 Submitter: Mihael H. Polymeropoulos MAP SUBMITTERS Name: Mihael H. Polymeropoulos Lab: Division of Intramural Research Institution: National Center for Human Genome Research Address: Bldg. 49, Room 4A-66, NIH, 8600 Rockville Pike, Bethesda, MD 20894 Tel: 301 402 2119 E-mail: mihael at helix.nih.gov MAP METHODS Method Name: Somatic Cell Hybridization: Polymeropoulos || From jamesjjcai at gmail.com Sat Jun 23 01:37:33 2007 From: jamesjjcai at gmail.com (James Cai) Date: Fri, 22 Jun 2007 22:37:33 -0700 Subject: [BiO BB] PGEToolbox -- Matlab toolbox for population genetics & evolution Message-ID: <5ce8fcf80706222237u30839c0cm93ff71191fe14c5a@mail.gmail.com> Dear All, PGEToolbox is a Matlab-based program for analysis of polymorphism and divergence data in population genetics and evolution. It computes basic statistics of DNA sequence variation and carries out neutrality tests, such as Tajima's D test, Fu & Li's tests and Fay & Wu's H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions), and also contains functions for handling SNP genotype and haplotype data. The latest version of the program can be obtained from: http://bioinformatics.org/pgetoolbox/ All the best, James J. Cai From wilfred at sdsc.edu Sat Jun 30 02:32:16 2007 From: wilfred at sdsc.edu (Wilfred Li) Date: Fri, 29 Jun 2007 23:32:16 -0700 Subject: [BiO BB] NBCR Summer Institute 2007 -- Cyberinfrastructure and Multiscale Modeling Approaches Message-ID: <452F37AE49199D49B1702D7D45038C4DA8CD1A@et.ad.sdsc.edu> Announcement: NBCR Summer Institute 2007 -- Cyberinfrastructure and Multiscale Modeling Approaches The National Biomedical Computation Resource (NBCR) is pleased to present its second annual Summer Institute to be held Jul 30 - August 3, 2007. This training program will provide an overview of cyberinfrastructure and multiscale modeling approaches, and will include a mini-symposium and hands-on training sessions using the tools essential for cutting edge biomedical research. NBCR's goal in offering this Summer Institute is to broaden the impact of these tools and work closely with the biomedical community in future developments, while offering significant opportunities for networking among researchers and participants. http://nbcr.net/si/ Training Sessions Each of the following topics represents a parallel track that will meet half days, for four days. Each participant may sign up for up to two tracks. Cluster and Grid Computing Programming Scalable Scientific Applications Computational cardiac electrophysiology and mechanics Molecular electrostatics and diffusion Molecular visualization and virtual screening Integrative Studies: Translational Biomedical Research Course Materials For online access of training session materials, please visit the 2006 NBCR Public Wiki or after the Summer Institute for 2007 materials. The workshop is geared toward graduate students, postdocs and researchers interested in learning how to use specific tools addressed by this workshop and/or who are interested in understanding the role of cyberinfrastructure in biomedical research. Important Dates For individuals who do not need housing, the registration deadline is July 23rd, and the costs are $400 for two tracks, or $250 for one track. For individuals who require housing and meals, the registration deadline is July 9th, and the costs are $660 (6 nights), plus $110 for each additional night. Registration fee is waived for out of town participants using campus lodging. All tracks are free to UCSD affiliated participants subject to space availability, with paying participants and those with accepted posters given higher priority. Scholarships There are a number of scholarships awarded to defray the costs of attending the meeting. Applicants are encouraged to apply early. The deadline for application is May 31, 2007. Notifications will be given by June 14, 2007. Please send your CV, poster abstract, and one letter of recommendation from or contact info for your Ph.D. advisor or immediate supervisor to Wilfred Li. An acknowledgment of receipt of your application will be sent within 2 days. If you don't receive such an email, please resend and contact Teri Simas as well. Awardees are required to present a poster during the poster sessions. Expenses are reimbursed after the event. Registration and pre-payment before the registration deadline is still required. For the names of the recipients of the 2006 Summer Institute, please visit the NBCR Summer Institute Forum. Schedule at a Glance Enrollment is limited. To ensure your place in the Summer Institute program and to help us accommodate you, we ask that you register as early as possible. May 31st, 2007, scholarship application June 14th, 2007, scholarship decision July 16th, campus housing and meals registration July 23rd, last day for registration July 30th, mini-symposium July 31 - Aug 3, training sessions. Aug 2, Conference Dinner and Certificate Ceremony. Please contact Teri Simas (858.534.5034, tgraysimas at ucsd.edu) for further information