From Reactome-Knowledgebase at reactome.org Thu Mar 1 14:32:54 2007 From: Reactome-Knowledgebase at reactome.org (Reactome-Knowledgebase at reactome.org) Date: Thu, 1 Mar 2007 14:32:54 -0500 Subject: [BiO BB] Reactome version 20 released Message-ID: Version 20 of the Reactome Knowledgebase has been released and is accessible at http://www.reactome.org! Reactome is a curated knowledgebase developed and maintained by the Reactome Knowledgebase team (Lincoln Stein's group at CSHL and Ewan Birney's group at European Bioinformatics Institute). Reactome covers human biological processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI, Entrez Gene, RefSeq, OMIM, Ensembl genome annotations, HapMap, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). New topics released in Version 20 are Fibroblast Growth Factor Receptor (FGFR) signaling, Epidermal Growth Factor Receptor (EGFR) signaling under signaling pathways, Gap junction trafficking under cell biology, and Porphyrin metabolism, Digestion of dietary carbohydrate and lipid under metabolic pathways. Additional events for HIV REV protein interactions, and Influenza virus RNP assembly have been added to corresponding infectious disease pathways. The standard display feature allows the user to choose the focus species annotations - curated (for human) and electronically inferred (for 22 other species). Updated release statistics and the Editorial Calendar are available. A SOAP based Web Services API is available aong with other resources to access the Reactome data from Download page. As before, Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused and redistributed freely. For questions and comments please reply to this message or write to help at reactome.org -Gopal Gopinathrao Reactome, CSHL From amonti at unich.it Fri Mar 2 14:33:25 2007 From: amonti at unich.it (Andrea Monti) Date: Fri, 02 Mar 2007 20:33:25 +0100 Subject: [BiO BB] Conference announcing - Italian Biotech Law Conference 2007 Message-ID: <45E87C05.3050701@unich.it> Dear All, The Italian Biotech Law Conference 2007 will start next Apr. 5, 07 in Milan, at the IFOM-FIRM research facilties. The conference topic is "Who owns bioinformation". Here is the programme - http://www.iblc.it/program.php Conference background WHAT IS IBLC IBLC stands for Italian Biotech Law Conference, the first Italian scientific conference dealing, from an interdisciplinary perspective, with life-science, information technology and law. IBLC ?father? is Andrea Monti (www.andreamonti.net) , an Italian lawyer and legal scholar, researching, since more than 12 years, the field of ICT legal issues. IBLC was born in 2004 as an Italian Cyberspace Law Conference (www.iclc.org) ?spinoff?, with title Bioinformatics Research between IP protection and information free flow. The discussant where dr. Marcella Attimonelli (associate professor of molecular biology at the University of Bari) and dr. Paolo Vezzoni (researcher at the National Research Council?s Institute of Biomedical Technologies). IBLC second edition (2005) the title Protection of Biotech Assets, Market, Freedom of Research has been discussed by dr. Enrico Dainese (associate professor at Teramo University?s Comparative Biomedical Science Dept.), dr. Giampiero Di Plinio (professor of Public Comparative Law at the University of Chieti), dr. Piero Fariselli (researcher at the Department of Biology - University of Bologna), dr. Andrea Cocito (FIRC Foundation of Molecular Oncology?s bioinformatics group.) Who owns bioinformation? is the IBLC 2007 Third edition leading question. (Possible) answers come from the following high profile scholars and researchers, ?managed? by Giovanni Boniolo (conference chair - University of Padova, IT, Dept. of Philosophy): Pier Paolo Di Fiore - Andrea Cocito FIRC - IFOM - How to build bioinformation Luciano Floridi Oxford University, Oxford, UK - What is bioinformation Giovanni Ziccardi - University of Milan, IT - Semantic Ambiguities, Intellectual Propriety, Law Marco Ventura - University of Siena, IT - Bioinformation and Public Policies IBLC 2007 is hosted by IFOM-FIRC Foundation of Molecular Oncology (www.ifom-firc.it) at its Milan research facilities, 16, via Adamello. From lichunjiang at sibs.ac.cn Mon Mar 5 02:41:47 2007 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Mon, 5 Mar 2007 15:41:47 +0800 (CST) Subject: [BiO BB] anyone know how to get the promoter sequence of mouse gene In-Reply-To: <200702271448.l1REmcVY014901@mailhub-4.iastate.edu> References: <2681.198.82.30.149.1172433768.squirrel@webmail.vbi.vt.edu> <76f031ae0702270632t2bd41a4yaa1700b3468abd31@mail.gmail.com> <200702271448.l1REmcVY014901@mailhub-4.iastate.edu> Message-ID: <1337.10.10.224.28.1173080507.squirrel@webmail.sibs.ac.cn> Hi Yan, ????? Maybe cisRED which is available from http://www.cisred.org/ and PROMSER which is available from http://cagt.bu.edu/page/Promoser_about are helpful for you. Good Luck! Lichun Li Xue wrote: > Hi Yan, > > The following link is to predict promoter region for barley probeset. > It is different from your problem in that servers offered are mainly > plant genome, but may offer some clue of the steps. > http://gremlin1.gdcb.iastate.edu/~volker/teaching/bcb594.html > > Li > > At 08:32 AM 2/27/2007, you wrote: >>googling for mouse and promoter gives you this as first hit: >>http://rulai.cshl.edu/CSHLmpd2/ >>batch queries are possible as far as I remember. >> >>cheers, >>Max >>On 25/02/07, yzhang at vbi.vt.edu wrote: >>>anyone know if I have a mouse gene(or human gene)'s gene accession #, >>> how >>>could I use this number to get promotor sequence of this gene? or >>> -1000bp >>>sequence? How about batch query? >>>best >>>yan >>> >>>_______________________________________________ >>>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 >> > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences From b.d.vanschaik at amc.uva.nl Fri Mar 9 09:49:22 2007 From: b.d.vanschaik at amc.uva.nl (B.D.C. van Schaik) Date: Fri, 09 Mar 2007 15:49:22 +0100 Subject: [BiO BB] 4th International Symposium on Networks in Bioinformatics (ISNB)/2nd Netherlands Bioinformatics Conference (NBIC) Message-ID: <11921291192e15.1192e151192129@amc.uva.nl> NBIC-ISNB 2007 2nd Netherlands Bioinformatics Conference (NBIC) 4th International Symposium on Networks in Bioinformatics (ISNB) 16-19 April 2007, Amsterdam, the Netherlands http://www.nbic-isnb2007.eu/ You are invited to register and submit an abstract for a contributed talk, a poster or the application showcase. Deadline for registration and abstracts: March 15. NBIC-ISNB 2007 is a four-day international bioinformatics conference that includes: - 2nd Netherlands Bioinformatics Conference (NBIC) - 4th International Symposium on Networks in Bioinformatics (ISNB) - Launch of the Dutch Computational Life Sciences research programme (CLSII) - Master Class bioinformatics - Application showcase 2nd Netherlands Bioinformatics Conference (NBIC) The Netherlands Bioinformatics Conference is an initiative of the Netherlands Bioinformatics Centre (NBIC). NBIC aims to strengthen and support the bioinformatics community in the Netherlands through the initiation of bioinformatics programmes and the organization of events. The 2nd NBIC meeting (16-17 April) will start with invited lectures on the special theme protein structure, one of the oldest themes in bioinformatics. Internationally acknowledged speakers will discuss how we can understand protein function and protein interaction from 3D structure. 4th International Symposium on Networks in Bioinformatics (ISNB) ISNB (17-19 April) focuses on the bioinformatics of biological networks which involves a range of interconnected multidisciplinary research topics. Research areas include the quantitative understanding of the dynamics of regulatory and metabolic networks by using modeling and simulation techniques, the reconstruction of biological pathways from experimental data, identification of pathway modules, the analysis and interpretation of experimental data in the context of biological networks, the construction and use of (public) pathway databases, network visualization and the development and use of pathway markup languages. Biological questions and new experimental techniques as well as ongoing efforts in (bio)informatics and statistics guide the development of the next generation of computational methodologies. The combination of computational and genomics research will accelerate the detailed understanding of biological networks, which will find many applications in all application domains of life sciences. Application showcase Many bioinformatics projects are aimed at developing specialized software tools and databases. On Monday at this conference, NBIC organizes an Application Showcase. You are invited to submit an abstract describing your software tool or database. This abstract will be included in the conference proceedings. A committee makes a selection of abstracts to be invited for a (live) demonstration to the bioinformatics community in the Netherlands during the NBIC conference. Relevance, originality and usability will be among the selection criteria. The conference participants will also be invited to vote for their favourite application. The winning application will be rewarded with a prize. Confirmed speakers NBIC - Dr Rob Russell Structural Bioinformatics Group, EMBL, Heidelberg, Germany - Dr Ruben Abagyan Ruben Abagyan Research Group, The Scripps Research Institute, La Jolla, USA - Prof dr Gianni Cesareni Department of Biology, University of Rome Tor Vergata, Rome, Italy Confirmed speakers ISNB - Dr Sally Leys, Department of Biological Sciences, University of Alberta, Canada - Dr Bernard Degnan, Integrative Biology, University of Queensland, Australia - Dr Sylvie Tambutt?, Centre Scientifique de Monaco, Monaco - Dr Mikhail Matz, Integrative Biology, University of Texas at Austin, USA - Dr Andreas Beyer, Department of Bioengineering, University of California San Diego, USA - Dr John Finnerty, Boston University, USA - Prof Matthias Mann, Department of Proteomics and Signal Transduction Max-Planck Institute for Biochemistrty, Martinsried, Germany - Dr Yair Field, Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel - Dr Edmund J. Crampin, Auckland BIoengineering Institute, The University of Auckland, New Zealand - Dr Hans van Beek, Free University, Amsterdam, the Netherlands -- Barbera D.C. Danz - van Schaik Email: B.D.vanSchaik at amc.uva.nl Bioinformatics Laboratory Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB) Room: J1B.205 (mon, thu, fri) Phone: (+31) 20 - 566 47 11 Department of Human Genetics Room: M1.131 (tue, wed) Phone: (+31) 20 - 566 65 92 Academic Medical Center / University of Amsterdam PO Box 22660 (J1B.205) 1100 DD Amsterdam The Netherlands From yan.shuangchun at gmail.com Wed Mar 14 15:48:47 2007 From: yan.shuangchun at gmail.com (Jeremy Yan) Date: Wed, 14 Mar 2007 15:48:47 -0400 Subject: [BiO BB] Calculate pairwise DNA percent identity in a set of data Message-ID: Hello, I need a software that can calculate pairwise DNA percent identity. I know MegAlign from DNAStar can do it, but it can only give you one decimal which is not enough for me. I have ever used a command line program to do it and get up to 5 decimal, such as "0.95488". But after a day of searching, I could not find out which program I used. The kind of percent identity is just something for very similar sequences. I have 18 sequences, no gap, they have percent identity from approximately 95%-99.x%. I need a more accurate percentage to calculate any pair of sequence, how many mismatch there are, i.e. the number of nucleotide differences. So if there is any software can just count how the number of nucleotide differences between any pair of sequences in a set of data, that works as well. Thank you very much for the help! Jeremy From clement at cs.byu.edu Thu Mar 15 12:16:43 2007 From: clement at cs.byu.edu (Mark Clement) Date: Thu, 15 Mar 2007 10:16:43 -0600 Subject: [BiO BB] International Symposium on Bioinformatics & Bioengineering (BIBE 2007) Message-ID: <6B2F86B5-D661-432D-B46B-68157087978F@cs.byu.edu> We would like to invite you to submit a paper to a special session of the International Symposium on Bioinformatics & Bioengineering (BIBE 2007) devoted to sequence alignment and phylogenetic analysis. This session will provide a venue where current algorithms can be examined and new algorithms can be presented. We would like to see a good mix of papers from computational tool developers and biologists who use these tools to make new discoveries. The Symposium will be held in Boston Massachusetts October 15-17, 2007 Papers should be submitted through the normal online submission process found at http://www.cs.gsu.edu/BIBE07/submission.php The submission deadline is May 15, 2007. Papers from other Bioinformatics areas can be submitted through this same page. More information about the Symposium can be found at http://www.cs.gsu.edu/BIBE07/index.php ---------------- Dr. Mark Clement Department of Computer Science Brigham Young University 2216 TMCB Provo, Utah 84602 (801) 422-7608 clement at cs.byu.edu From lixue at iastate.edu Fri Mar 16 12:32:18 2007 From: lixue at iastate.edu (Li Xue) Date: Fri, 16 Mar 2007 11:32:18 -0500 Subject: [BiO BB] how to build a prediction website Message-ID: <200703161632.l2GGWPMm030881@mailhub-5.iastate.edu> Hello all, I want to write my interface prediction algorithm into a website so that the user can submit a protein sequence and get the prediction results online. I have never build a website before. Would you please recommend what language should I use and what procedure should I follow? Thank you. Li From hlapp at gmx.net Sat Mar 17 10:07:19 2007 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 17 Mar 2007 10:07:19 -0400 Subject: [BiO BB] Phyloinformatics Summer of Code Message-ID: Phyloinformatics Summer of Code 2007 A collaborative Phyloinformatics Group, sponsored by the National Evolutionary Synthesis Center (NESCent: http://www.nescent.org/), is working to develop user-interfaces, improve software interoperability and support data exchange standards in evolutionary bioinformatics. The specific projects are diverse in nature and range from the development of AJAX components for web-based bioinformatics applications, managing workflows using approaches from functional and logic programming, and developing data exchange standards for phylogenetic substitution models. The Phyloinformatics group will be sponsoring student collaborators through the Google Summer of Code program (http://code.google.com/ soc), which provides undergraduate, masters and PhD students with a unique opportunity (over three summer months) to obtain hands-on experience writing and extending open-source software under the mentorship of experienced developers from around the world. We are particularly targeting students interested in both evolutionary biology and software development. Students will have one or more dedicated mentors with expertise in phylogenetic methods and open- source software development. Our project proposals are flexible and can be adjusted in scope to match the skills of students with less programming proficiency. If the program sounds interesting to you but you are unsure whether you have the necessary skills, please email the mentors at phylosoc {at} nescent {dot} org. We will work with those who are genuinely interested to find a project that fits your interest and skills. Students will receive a stipend from Google and will be invited to participate in future collaborative events such as the NESCent Phyloinformatics Hackathons (http://www.nescent.org/wg/ phyloinformatics). TO APPLY: Students must apply on-line at the Google Summer of Code website (http://code.google.com/soc). The application period for students is now open and ends on Saturday, March 24, 2007 (one week from now). The Phyloinformatics Summer of Code project and ideas page is at the following URL: http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2007 The above page also contains links to the GSoC program rules, eligibility requirements, and stipend payment mechanism. We encourage all interested students to email any questions, or self-proposed project ideas, to phylosoc {at} nescent {dot} org. This will reach all prospective mentors. Eligibility requirements for students: http://code.google.com/support/bin/answer.py?answer=60279&topic=10730 Stipend for students: http://code.google.com/support/bin/answer.py?answer=60322&topic=10731 Please disseminate this announcement to appropriate students at your institution. Hilmar Lapp Assistant Director for Informatics NESCent From amonti at unich.it Sat Mar 17 12:14:27 2007 From: amonti at unich.it (Andrea Monti) Date: Sat, 17 Mar 2007 17:14:27 +0100 Subject: [BiO BB] how to build a prediction website In-Reply-To: <200703161632.l2GGWPMm030881@mailhub-5.iastate.edu> References: <200703161632.l2GGWPMm030881@mailhub-5.iastate.edu> Message-ID: <45FC13E3.2030208@unich.it> Hello Li Xue To build a website you need to choose: 1 - the evironment (personally, I like FreeBSD, is robust and secure, but Linux too is an option) 2 - a web server (suggestion: Apache2) 3 - a programming language (Perl should fit your needs. If you want to handle a data-base, then the "dynamic duo" is MySQL/PHP) 4 - a text editor (plenty of that under all platform: dana for windows, textwrangler for MacOSX, emacs for *NIX) You also need to host your website, then you should look for a static IP or a (sub)domain and a computer that hosts the site. Hope that helps. Andrea Monti Li Xue wrote: > Hello all, > > I want to write my interface prediction algorithm into a website so > that the user can submit a protein sequence and get the prediction > results online. > > I have never build a website before. > > Would you please recommend what language should I use and what > procedure should I follow? Thank you. > > > Li > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lixue at iastate.edu Mon Mar 19 16:09:57 2007 From: lixue at iastate.edu (Li Xue) Date: Mon, 19 Mar 2007 15:09:57 -0500 Subject: [BiO BB] how to build a prediction website In-Reply-To: <45FC13E3.2030208@unich.it> References: <200703161632.l2GGWPMm030881@mailhub-5.iastate.edu> <45FC13E3.2030208@unich.it> Message-ID: <200703192009.l2JK9vDS022798@mailhub-5.iastate.edu> Thank you, Andrea. That really help! Li At 11:14 AM 3/17/2007, you wrote: >Hello Li Xue > >To build a website you need to choose: > >1 - the evironment (personally, I like FreeBSD, is robust and secure, >but Linux too is an option) >2 - a web server (suggestion: Apache2) >3 - a programming language (Perl should fit your needs. If you want to >handle a data-base, then the "dynamic duo" is MySQL/PHP) >4 - a text editor (plenty of that under all platform: dana for windows, >textwrangler for MacOSX, emacs for *NIX) >You also need to host your website, then you should look for a static IP >or a (sub)domain and a computer that hosts the site. > >Hope that helps. >Andrea Monti > >Li Xue wrote: > > Hello all, > > > > I want to write my interface prediction algorithm into a website so > > that the user can submit a protein sequence and get the prediction > > results online. > > > > I have never build a website before. > > > > Would you please recommend what language should I use and what > > procedure should I follow? Thank you. > > > > > > Li > > > > > > > > _______________________________________________ > > 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 Xue, Li Bioinformatics and Computational Biology Program Iowa State University 1-515-5201676 From varvenne at genoway.com Tue Mar 20 10:48:03 2007 From: varvenne at genoway.com (Benoit VARVENNE) Date: Tue, 20 Mar 2007 15:48:03 +0100 Subject: [BiO BB] EST vs cDNA reliability Message-ID: Hello to all, I've got some troubles finding information about the difference of reliability we should give to ESTs vs. the one given to cDNAs while determining a gene structure. Can anyone help me understand how each of these are built (papers ?, ...), in order to understand how we should consider each of them ? I'd be very greatful to you if you could... Cheers Benoit From me_lily at msn.com Mon Mar 19 16:57:03 2007 From: me_lily at msn.com (lily xue) Date: Mon, 19 Mar 2007 20:57:03 +0000 Subject: [BiO BB] how to visit NCBI Blast and get the plain text result using script Message-ID: Hello all, Would you please tell me whether it is possible for me to write some script (maybe perl script) to call NCBI Blast and get the plain text result from my own computer? Thanks. Lily _________________________________________________________________ Don't just search. Find. Check out the new MSN Search! http://search.msn.com/ From jeff at bioinformatics.org Tue Mar 20 22:31:10 2007 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 20 Mar 2007 22:31:10 -0400 Subject: [BiO BB] Tuition waivers available for Bioinformatics.Org courses Message-ID: <460098EE.2010804@bioinformatics.org> Bioinformatics.Org is offering 5 tuition waivers for the online course BI201B Microarray Data Analysis, Part 2: SNP Genotyping, March 26-30, 2007. This means that 5 people will be able to take this tuition-based, week-long course and receive a certificate of completion from Bioinformatics.Org, all for free. COURSE OBJECTIVE: This course helps to demystify Affymetrix analysis so that any researcher can take the basic steps to go from a chip image to genotypes, for each SNP, and to the copy number or linkage associated with the SNPs in given samples. Various tools will be covered, such as GCOS, GTYPE, BRLMM, CNAT, Excel, MATLAB, and free tools like Dchip. Please note that the live lectures take place between 15:30 and 18:30 UTC (GMT), which is in the middle of the night for Asia and the Pacific islands. However, the lectures are recorded in reduced resolution and can be viewed the following day, each day. MORE INFORMATION ON THE COURSE: http://edu.bioinformatics.org/AO QUALIFICATIONS & HOW TO APPLY: Acceptance will be based on the following criteria: 1. Applicants for the waivers must be residing in one of the following nations and territories (taken from the World Bank's 2004 list of low and lower-middle income economies) and be a citizen or legal resident of the respective nation: Afghanistan Macedonia Albania Madagascar Algeria Malawi Angola Maldives Armenia Mali Azerbaijan Marshall Islands Bangladesh Mauritania Belarus Micronesia Benin Moldova Bhutan Mongolia Bolivia Morocco Bosnia and Herzegovina Mozambique Brazil Myanmar Bulgaria Namibia Burkina Faso Nepal Burundi Nicaragua Cambodia Niger Cameroon Nigeria Cape Verde Pakistan Central African Republic Papua New Guinea Chad Paraguay China Peru Colombia Philippines Comoros Romania Congo Russia Cuba Rwanda Djibouti Samoa Dominican Republic Senegal Ecuador Sierra Leone Egypt Solomon Islands El Salvador Somalia Equatorial Guinea South Africa Eritrea Sri Lanka Ethiopia Sudan Fiji Suriname Gambia Swaziland Georgia S?o Tom? and Principe Ghana Tajikistan Guatemala Tanzania Guinea Thailand Guinea-Bissau Timor-Leste Guyana Togo Haiti Tonga Honduras Tunisia India Turkey Indonesia Turkmenistan Iran Uganda Iraq Ukraine Ivory Coast Uzbekistan Jamaica Vanuatu Jordan Vietnam Kazakhstan West Bank and Gaza Kenya Yemen Kiribati Zambia Korea, North Zimbabwe Kyrgyz Republic Lao Lesotho Liberia Since there isn't time for verification of residence via postal mail, the applicant must submit the research statement mentioned below from an IP address that resolves (via reverse lookup) to a postal address in one of these nations (i.e., don't use a yahoo.com or hotmail.com account). 2. Applicants must demonstrate proficiency in English and science by submitting a 300- to 500-word statement of research interests, including how the course content is related to their research, to edu at bioinformatics.org 3. Applicants must have daily access to a computer with an Internet connection that has a transfer speed in excess of 768 kbps, such as at a university or an Internet cafe. This is required for viewing the live or recorded lectures. DEADLINE: Saturday NOTICE OF ACCEPTANCE: Sunday Applications will be kept on file for consideration for future courses. If you have any questions, please write to edu at bioinformatics.org Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From marchywka at hotmail.com Wed Mar 21 00:21:18 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 21 Mar 2007 00:21:18 -0400 Subject: [BiO BB] looking for potentials for molecule simulations Message-ID: Hi, After someone's suggestion earlier regarding opengl, I went ahead and wrote a molecule viewer ( details below). I tested some modelling concepts using a simple 1/r potential and wanted to find some options for more realistic simulations. Anyone know off hand of particularly realistic model potentials, preferably only with parameters that can be derived from a pdb file :) I originally thought the interesting thing was going to be cavity modelling- all I've seen in this area is O. If anyone has a link to some nice cavity pictures or open topics in the area please let me know- I'm kind of looking for something useful to do with this code now :) The cavity outlines I've produced so far see to be accurate but lacking in any obvious usage. I was curious to see if I could characterize the active site of an enzyme well enough to get some idea of selectivity. Right now I just have pictures- some visually appealing but of no obvious use yet. And, yes, I did check google first but as you can imagine it is a big area... http://en.wikipedia.org/wiki/Molecular_dynamics The above does list pymol, I guess I could lift some of their code even if I can't get the whole thing to build. fwiw, a few details: I wrote an opengl molecule viewer using C++-. I was able to display and outline the inner cavity for a proteasome and manipulate some other macromolecules. The C++ STL containers and opengl make everything pretty easy. I won't claim it has as many niceties as RasMol yet, but the data structures should give me some flexibility for later. I originally ddn't think it would be worth the effort but I couldn't immediately get pymol to build under cygwin so I thought I would give it a try and now think it may be worthwhile. Thanks. _________________________________________________________________ Live Search Maps ? find all the local information you need, right when you need it. http://maps.live.com/?icid=hmtag2&FORM=MGAC01 From christoph.gille at charite.de Wed Mar 21 05:58:42 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 21 Mar 2007 10:58:42 +0100 (CET) Subject: [BiO BB] how to visit NCBI Blast and get the plain text result using script In-Reply-To: References: Message-ID: <48439.141.42.56.114.1174471122.squirrel@webmail.charite.de> I have done this EBI blast. I guess it is also possible NCBI. You can get it in computer readable form (XML) or in human readable form. Your script needs to send the POST data i.e. the query sequence and the other settings. Check the man pages of wget or w3m for this. Depending on your favorite computer language you can use tool-kits. They make thinks much more convenient for you. I would highly recomend to use one of those. Python: Biopython, Perl: Bioperl, Java: STRAP, Biojava Ruby: BioRuby Good luck! Christoph From christoph.gille at charite.de Wed Mar 21 06:00:13 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 21 Mar 2007 11:00:13 +0100 (CET) Subject: [BiO BB] how to visit NCBI Blast and get the plain text result using script In-Reply-To: References: Message-ID: <48442.141.42.56.114.1174471213.squirrel@webmail.charite.de> I have done this EBI blast and I guess that it is also easily possible with NCBI. You can get it in computer readable form (XML) or in human readable form. Your script needs to send the POST data i.e. the query sequence and the other settings. Check the man pages of wget or w3m for this. Depending on your favorite computer language you can use tool-kits. They make thinks much more convenient for you. I would highly recomend to use one of those. Python: Biopython, Perl: Bioperl, Java: STRAP, Biojava Ruby: BioRuby Good luck! Christoph From marchywka at hotmail.com Wed Mar 21 08:07:12 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 21 Mar 2007 08:07:12 -0400 Subject: [BiO BB] how to visit NCBI Blast and get the plain text result using script In-Reply-To: <48442.141.42.56.114.1174471213.squirrel@webmail.charite.de> Message-ID: I did that originally before finding out about eutils- it is good practice but the eutils support is definitely the way to go. They even have examples. I have some scripts I can send you or see my prior posts ( I was using an address from eyewonder.com in the past). In any case, see some of these links: UTILS="http://www.ncbi.nlm.nih.gov/entrez/eutils" UTILS="http://eutils.ncbi.nlm.nih.gov/entrez/eutils" #http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html #http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html ESEARCH="$UTILS/esearch.fcgi?tool=biotechmarchywka&email=marchywka at hotmail.com&db=$db&retmax=1&usehistory=y$EXTRASTUFF&${THETERM}=" efetch="$UTILS/efetch.fcgi?tool=biotechmarchywka&email=marchywka at hotmail.com&rettype=$report&retmode=$retmode&retstart=$retstart&retmax=$retmax&db=$db&query_key=$QueryKey&WebEnv=$WebEnv" This compares well to trying to use their web interface: RLFORM="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed" POSTDATA="WebEnv=0tkD70MRHDOu0sYn3uzuCoQig9Q1pFy0V7rMPPSVjt2KvOTKNujp&db=pubmed&orig_db=pubmed&term=dna&inputpage=3&cmd=search&cmd_current=" LYNXCMD="lynx -accept_all_cookies -cookie_file=${OLDCOOKIES} -cookie_save_file=${COOKIEJAR} -dump -post_data" echo ${POSTDATA} |${LYNXCMD} ${URLFORM} But these approaches diverge even more when you actually try to use the results- structured abstracts in a tractable format versus trying to parse html... I think their web interface does have a text format but this still is only a partial solution. http://www.ncbi.nlm.nih.gov/entrez/queryd.fcgi?CMD=search&DB=pubmed ( note new address as of 10-06) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165r ( NOTE MORE NEWER NUMBER ) 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only >From: "Dr. Christoph Gille" >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] how to visit NCBI Blast and get the plain text result >using script >Date: Wed, 21 Mar 2007 11:00:13 +0100 (CET) > >I have done this EBI blast and >I guess that it is also easily possible with NCBI. >You can get it in computer readable form (XML) or in >human readable form. >Your script needs to send the POST data i.e. the >query sequence and the other settings. >Check the man pages of wget or w3m for this. >Depending on your favorite computer language you >can use tool-kits. They make thinks much more convenient >for you. I would highly recomend to use one of those. >Python: Biopython, >Perl: Bioperl, >Java: STRAP, Biojava >Ruby: BioRuby >Good luck! >Christoph > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Exercise your brain! Try Flexicon. http://games.msn.com/en/flexicon/default.htm?icid=flexicon_hmemailtaglinemarch07 From dgw106 at york.ac.uk Wed Mar 21 10:13:21 2007 From: dgw106 at york.ac.uk (David) Date: 21 Mar 2007 14:13:21 +0000 Subject: [BiO BB] how to visit NCBI Blast and get the plain text result using script In-Reply-To: References: Message-ID: Dear Lily, You can download and run BLAST locally to save network traffic, if you prefer, especially if you have many queries to run. Binaries are available for many platforms at http://www.ncbi.nlm.nih.gov/BLAST/. Of course, you need space to store the databases. For example, the non-redundant protein sequence database is a few hundred MB I think... Parsing BLAST XML output (using the option '-m 7' when running BLAST from the command line) can be done easily using the NCBIXML module in Biopython. This method has the feature that you have a static BLAST version and database, so allows for reproducibility, which can be viewed as an advantage or disadvantage, depending what you want to do. Cheers David On Mar 21 2007, lily xue wrote: >Hello all, > > Would you please tell me whether it is possible for me to write some > script (maybe perl script) to call NCBI Blast and get the plain text > result from my own computer? Thanks. > >Lily > >_________________________________________________________________ >Don't just search. Find. Check out the new MSN Search! >http://search.msn.com/ > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From marchywka at hotmail.com Wed Mar 21 11:45:09 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 21 Mar 2007 11:45:09 -0400 Subject: [BiO BB] how to visit NCBI Blast and get the plain text resultusing script In-Reply-To: Message-ID: ftp://ftp.ncbi.nih.gov/blast/documents/ As for the earlier issue,you can compare executing a binary: echo -e ">${NAME}\n${SEQ}\n" | blastcl3 ${BL} > .temp_blastnew_1 To trying to work around the web interface:: QS1="QUERY=${SEQ}" QS2="&QUERY_FROM=&QUERY_TO=&DATABASE=nr&ENTREZ_QUERY=&ENTREZ_QUERY=All+organisms&COMPOSITION_BASED_STATISTICS=0" QS3="&EXPECT=${expect}&WORD_SIZE=2&MATRIX_NAME=PAM30&GAPCOSTS=9+1&PSSM=&OTHER_ADVANCED=&PHI_PATTERN=&SHOW_OVERVIEW=on" QS4="&SHOW_LINKOUT=on&GET_SEQUENCE=on&NCBI_GI=on&FORMAT_OBJECT=Alignment&FORMAT_TYPE=${format}&MASK_CHAR=0&MASK_COLOR=0" QS5="&DESCRIPTIONS=1000&ALIGNMENTS=1000&ALIGNMENT_VIEW=Pairwise&I_THRESH=0.005&FORMAT_ENTREZ_QUERY=" QS6="&FORMAT_ENTREZ_QUERY=All+organisms&EXPECT_LOW=&EXPECT_HIGH=&LAYOUT=TwoWindows&FORMAT_BLOCK_ON_RESPAGE=None" QS7="&AUTO_FORMAT=Semiauto&PROGRAM=blastp&CLIENT=web&SERVICE=plain&PAGE=Proteins&CMD=Put" QUERYSTR="${QS1}${QS2}${QS3}${QS4}${QS5}${QS6}${QS7}" POSTURL="http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi" LYNXCMD="lynx -width=0 -source -accept_all_cookies -dump -post_data " echo $QUERYSTR | lynx -width=0 -source -accept_all_cookies -dump -post_data "${POSTURL}" > .temp_blast_0 >From: David >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] how to visit NCBI Blast and get the plain text >resultusing script >Date: 21 Mar 2007 14:13:21 +0000 > >Dear Lily, > >You can download and run BLAST locally to save network traffic, if you >prefer, especially if you have many queries to run. Binaries are available >for many platforms at http://www.ncbi.nlm.nih.gov/BLAST/. Of course, you >need space to store the databases. For example, the non-redundant protein >sequence database is a few hundred MB I think... > >Parsing BLAST XML output (using the option '-m 7' when running BLAST from >the command line) can be done easily using the NCBIXML module in Biopython. > >This method has the feature that you have a static BLAST version and >database, so allows for reproducibility, which can be viewed as an >advantage or disadvantage, depending what you want to do. > >Cheers >David _________________________________________________________________ Mortgage refinance is hot 1) Rates near 30-yr lows 2) Good credit get intro-rate 4.625%* https://www2.nextag.com/goto.jsp?product=100000035&url=%2fst.jsp&tm=y&search=mortgage_text_links_88_h2a5f&s=4056&p=5117&disc=y&vers=743 From ica28711 at nifty.com Tue Mar 20 23:19:54 2007 From: ica28711 at nifty.com (ica28711 at nifty.com) Date: Wed, 21 Mar 2007 12:19:54 +0900 (JST) Subject: [BiO BB] how to visit NCBI Blast and get the plain text result using script Re: NCBI BLAST mpiBLAST.org Message-ID: <18325376.46101174447194392.ica28711@nifty.com> From: "Kenta Sato" ICA28711 at nifty.com ARP1 To: "lily" me_lily at msn.com I received your e-mail NCBI Blast txt. message. In reply, I suggest this proce dure, open search on Web support www.mpiblast.org browse Virginia Tech, University o f Utah, and North Carolina State University SC|06 458 lines on ad-hoc grid, but - I recommend to wait using mpiBLAST-1.4.0-pio.tgz because of unknown PC memory size on MD5 sum cryptographic signiture which requires scalable informa - tics of msn 47 byte and stable. Kenta Sato ARP1 Tel: 81-466-50-1916 Fax: 81-466-50-1916 E-mail: ICA28711 at nifty.com http://www.home.ne.jp ----- Original Message ----- >From: "lily xue" >To: bio_bulletin_board at bioinformatics.org >Date: Mon, 19 Mar 2007 20:57:03 +0000 >Subject: [BiO BB] how to visit NCBI Blast and get the plain text result > using script > > >Hello all, > >Would you please tell me whether it is possible for me to write some script >(maybe perl script) to call NCBI Blast and get the plain text result from my >own computer? Thanks. > >Lily > >_________________________________________________________________ >Don't just search. Find. Check out the new MSN Search! >http://search.msn.com/ > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From aloraine at gmail.com Wed Mar 21 17:31:24 2007 From: aloraine at gmail.com (Ann Loraine) Date: Wed, 21 Mar 2007 15:31:24 -0600 Subject: [BiO BB] how to visit NCBI Blast and get the plain text result using script In-Reply-To: <48442.141.42.56.114.1174471213.squirrel@webmail.charite.de> References: <48442.141.42.56.114.1174471213.squirrel@webmail.charite.de> Message-ID: <83722dde0703211431j517afcc4k2b1d2e8d6e155326@mail.gmail.com> Speaking of python, does anybody know how to get urllib in python to send POST data? I'm used to building URLs and opening them using urllib.urlopen, but have wondered how to send data via "post" as well as "get." Perhaps there is a good library available for this, besides urllib? Or maybe urllib has the ability to do this, and I have not been reading the docs carefully enough. A code snippet would be much appreciated! All the best, Ann On 3/21/07, Dr. Christoph Gille wrote: > I have done this EBI blast and > I guess that it is also easily possible with NCBI. > You can get it in computer readable form (XML) or in > human readable form. > Your script needs to send the POST data i.e. the > query sequence and the other settings. > Check the man pages of wget or w3m for this. > Depending on your favorite computer language you > can use tool-kits. They make thinks much more convenient > for you. I would highly recomend to use one of those. > Python: Biopython, > Perl: Bioperl, > Java: STRAP, Biojava > Ruby: BioRuby > Good luck! > Christoph > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Ann Loraine, Assistant Professor Departments of Genetics, Biostatistics, Computer and Information Sciences Associate Scientist, Comprehensive Cancer Center University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From christoph.gille at charite.de Wed Mar 21 18:12:45 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 21 Mar 2007 23:12:45 +0100 (CET) Subject: [BiO BB] Windows Vista Message-ID: <36277.141.42.56.114.1174515165.squirrel@webmail.charite.de> Since the release of the new Windows system I have been concerned that the Protein Workbench STRAP is not working properly on Vista. May be that I need to change a few things to make it ready for Vista. Could you please be so kind and check whether there are problems. Java-Web-start: http://www.charite.de/bioinf/strap/strap2.jnlp Home: http://3d-alignment.eu/ Many thanks Christoph From dan.bolser at gmail.com Thu Mar 22 02:41:55 2007 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 22 Mar 2007 07:41:55 +0100 Subject: [BiO BB] Windows Vista In-Reply-To: <36277.141.42.56.114.1174515165.squirrel@webmail.charite.de> References: <36277.141.42.56.114.1174515165.squirrel@webmail.charite.de> Message-ID: <2c8757af0703212341v2b239fe0y1b7590234aef459a@mail.gmail.com> On 21/03/07, Dr. Christoph Gille wrote: > Since the release of the new Windows system I have been > concerned that the Protein Workbench STRAP is not working properly > on Vista. > May be that I need to change a few things > to make it ready for Vista. Listen here... http://www.grc.com/SecurityNow.htm#83 For some interesting comments. > Could you please be so kind and check whether there are > problems. > Java-Web-start: http://www.charite.de/bioinf/strap/strap2.jnlp > Home: http://3d-alignment.eu/ > Many thanks > > Christoph > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- hello From danielucg at yahoo.com.br Fri Mar 23 15:07:08 2007 From: danielucg at yahoo.com.br (Daniel Xavier de Sousa) Date: Fri, 23 Mar 2007 12:07:08 -0700 (PDT) Subject: [BiO BB] Time execute blast and Memory Message-ID: <20070323190708.18364.qmail@web52404.mail.re2.yahoo.com> Hi for all, I?m executing the BLAST program and have knew stranger (I guess) time of execute with differences RAM memory. Same with less memory, the difference of total time between X memory and X/2 memory is little. Look: PROGRAM NCBI BLAST == DATABASE NR (1.8 GB) Memory *TIME * I/O *SWAP 1 GB RAM *0:03:01 *2610920 *9456 512 MB RAM *0:03:10 *2670376 *18128 256 MB RAM *0:03:35 *2713160 *21856 128 MB RAM *0:04:22 *2751120 *30640 64 MB RAM *0:05:30 *3050656 *64168 PROGRAM WUBLAST1.4 == DATABASE NR (1.8 GB) Memory *TIME *I/O *SWAP 1 GB RAM *0:12:14 *2496144 *0 512 MB RAM *0:13:37 *2500216 *0 256 MB RAM *0:13:29 *2502376 *1720 128 MB RAM *0:13:35 *2513432 *1760 64 MB RAM *0:13:57 *2546192 *51048 The difference using more memory, must be better. For exempla, there is little difference using 1 GB and 512 MB for a database of 1.8GB (NR). The little difference is more accentuated to WUblast 1.4 than NCIBI BLAST. So, I want help to two things: 1 ? It results is normal, to WUBlast1.4 and NCBIBlast? 2 ? What can I do to get more difference when I change my RAM memory? Thank very much, Daniel ***************************************************************** * Daniel Xavier de Sousa * * Mestrando em Inform?tica - PUC-Rio * * E-MAIL : dsousaARROBAinf.puc-rio.br * * Fone : +55 21 35271500 - 4543 * **************************************************************** __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ From ykalidas at gmail.com Fri Mar 23 15:21:54 2007 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Sat, 24 Mar 2007 00:51:54 +0530 Subject: [BiO BB] how to build a prediction website In-Reply-To: <200703161632.l2GGWPMm030881@mailhub-5.iastate.edu> References: <200703161632.l2GGWPMm030881@mailhub-5.iastate.edu> Message-ID: <5632703b0703231221l26a0db9fn2d0b351d7fe871ab@mail.gmail.com> Hi Li You may find the following files useful apache httpd-2.2.3 is easy to use. Download untar the file and carry out steps similar to the ones below. Now run the following 1. ./configure --prefix=~/test_web_service make make install 2. cd ~/test_web_service/ 3. 1. cd conf 2. Edit httpd.conf Change "User daemon" to "User " so that you can start the program conveniently in your login without becoming root. and similarly for "Group daemon" to "Group " Set "Listen " 4. cd ../bin apachectl -k start Now you can keep many html-forms in the "htdocs" directory. Once you are done with hello world setup, additional things can be added on.. On 3/16/07, Li Xue wrote: > > Hello all, > > I want to write my interface prediction algorithm into a website so > that the user can submit a protein sequence and get the prediction > results online. > > I have never build a website before. > > Would you please recommend what language should I use and what > procedure should I follow? Thank you. > > > Li > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas From marchywka at hotmail.com Fri Mar 23 18:10:46 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 23 Mar 2007 18:10:46 -0400 Subject: [BiO BB] how to build a prediction website In-Reply-To: <5632703b0703231221l26a0db9fn2d0b351d7fe871ab@mail.gmail.com> Message-ID: I did look into this but didn't bother to reply at the time. Your institution probably has some assistance available but you can get almost everything free- at least for non-commercial usage. For an html editor, there are things like Kompozer that come up on google- or you can get the adobe/macromedia tools. For OS, Debian is an option too if you don't like Windoze. Of course, once you have apache, you may want some cgi or a servlet engine too. I wouldn't ignore java as an interface between the server/web and your application. If you really JUST want to offer a server and don't want much hassle, you could just start a process that listens on whatever port you publish and not worry too much about a "web site" or a server with a bunch of html. It may be easier to send README and perl/bash files to people than edit html :) The basic web server connection and logging stuff is really nice of course and well worth the hassle ( connecting your app to a port probably isn't the way to go except in some special cases). But, personally, I think the graphic design becomes an infinite time sink pretty quickly. You could either make a complicated form and have people cut/paste files into a text box or just send a readme file and a script to anyone interested. As an in between scenario, you could set up some simple html with instructions on how to format requests as http gets and posts. If you have limited time and resources, it is probably easiest and even better to just distribute things as similar to your development tools as possible ( you probably created some scripts or other stuff to test your service, these are probably easier to publish than de novo javascript ). Personally the first thing I do with any web form is find a way to script around it if I am serious about repeat usage. It would be easier for many users if you just publish a script. >From: "Kalidas Yeturu" >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] how to build a prediction website >Date: Sat, 24 Mar 2007 00:51:54 +0530 > >Hi Li >You may find the following files useful _________________________________________________________________ Mortgage refinance is hot 1) Rates near 30-yr lows 2) Good credit get intro-rate 4.625%* https://www2.nextag.com/goto.jsp?product=100000035&url=%2fst.jsp&tm=y&search=mortgage_text_links_88_h2a5f&s=4056&p=5117&disc=y&vers=743 From marchywka at hotmail.com Fri Mar 23 18:15:35 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 23 Mar 2007 18:15:35 -0400 Subject: [BiO BB] Time execute blast and Memory In-Reply-To: <20070323190708.18364.qmail@web52404.mail.re2.yahoo.com> Message-ID: I'm not sure specifically what you want to know or what you already know but to give you some ideas of what is fast/slow on Intel, take a look at some of these: http://www.google.com/search?hl=en&q=ia32+optimization+memory+cache+site%3Aintel.com Not all memory is the same and constant cache misses can slow things down a lot. You could be amazed how important locality is to performance. >From: Daniel Xavier de Sousa >Reply-To: "General Forum at Bioinformatics.Org" > >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Time execute blast and Memory >Date: Fri, 23 Mar 2007 12:07:08 -0700 (PDT) > >Hi for all, > > > > > >I?m executing the BLAST program and have knew stranger (I guess) time >of execute with differences RAM memory. Same with less memory, the >difference of total >time between X memory and X/2 memory is little. > > > >Look: > > > > > >PROGRAM NCBI BLAST == DATABASE NR (1.8 GB) > > > > > >Memory *TIME * I/O *SWAP > > >1 GB RAM *0:03:01 *2610920 *9456 > > >512 MB RAM *0:03:10 *2670376 *18128 > > >256 MB RAM *0:03:35 *2713160 *21856 > > >128 MB RAM *0:04:22 *2751120 *30640 > > >64 MB RAM *0:05:30 *3050656 *64168 > > > > > >PROGRAM WUBLAST1.4 == DATABASE NR (1.8 GB) > > >Memory *TIME *I/O *SWAP > > >1 GB RAM *0:12:14 *2496144 *0 > > >512 MB RAM *0:13:37 *2500216 *0 > > >256 MB RAM *0:13:29 *2502376 *1720 > > >128 MB RAM *0:13:35 *2513432 *1760 > > >64 MB RAM *0:13:57 *2546192 *51048 > > > > > >The difference using more memory, must be better. For >exempla, there is little difference using 1 GB and 512 MB for a database of >1.8GB (NR). The little difference is more accentuated to WUblast 1.4 than >NCIBI >BLAST. > > > > > >So, I want help to two things: > > >1 ? It results is normal, to WUBlast1.4 and NCBIBlast? > > >2 ? What can I do to get more difference when I change my >RAM memory? > > > > > > > > >Thank very much, > > >Daniel > >***************************************************************** >* Daniel Xavier de Sousa * >* Mestrando em Inform?tica - PUC-Rio * >* E-MAIL : dsousaARROBAinf.puc-rio.br * >* Fone : +55 21 35271500 - 4543 * >**************************************************************** > > > >__________________________________________________ >Fale com seus amigos de gra?a com o novo Yahoo! Messenger >http://br.messenger.yahoo.com/ >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Mortgage refinance is hot 1) Rates near 30-yr lows 2) Good credit get intro-rate 4.625%* https://www2.nextag.com/goto.jsp?product=100000035&url=%2fst.jsp&tm=y&search=mortgage_text_links_88_h2a5f&s=4056&p=5117&disc=y&vers=743 From lixue at iastate.edu Sat Mar 24 08:58:17 2007 From: lixue at iastate.edu (Li Xue) Date: Sat, 24 Mar 2007 07:58:17 -0500 Subject: [BiO BB] how to process a bunch of fasta sequences Message-ID: <200703241258.l2OCwQxG027126@mailhub-5.iastate.edu> Hello all, I am building an interface prediction website. Would you please suggest how to process a bunch of fasta sequences which is input by the users? My script is written in Perl. Should I use parellel computer or simply repeatedly call my script? Thank you. Xue, Li Bioinformatics and Computational Biology Program Iowa State University 1-515-5201676 From christoph.gille at charite.de Sat Mar 24 10:18:38 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Sat, 24 Mar 2007 15:18:38 +0100 (CET) Subject: [BiO BB] how to process a bunch of fasta sequences In-Reply-To: <200703241258.l2OCwQxG027126@mailhub-5.iastate.edu> References: <200703241258.l2OCwQxG027126@mailhub-5.iastate.edu> Message-ID: <61021.84.190.4.67.1174745918.squirrel@webmail.charite.de> The user could enter a multiple fasta file into the textarea of your Web form From golharam at umdnj.edu Sat Mar 24 15:11:57 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Sat, 24 Mar 2007 14:11:57 -0500 Subject: [BiO BB] how to process a bunch of fasta sequences In-Reply-To: <61021.84.190.4.67.1174745918.squirrel@webmail.charite.de> Message-ID: <009801c76e48$4b70c1d0$2e01a8c0@PICO> Have you looked at using bioperl? www.bioperl.org >-----Original Message----- >From: >bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.or >g >[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinform >atics.org] On Behalf Of Dr. Christoph Gille >Sent: Saturday, March 24, 2007 9:19 AM >To: General Forum at Bioinformatics.Org >Subject: Re: [BiO BB] how to process a bunch of fasta sequences > > >The user could enter a multiple fasta file >into the textarea of your Web form > >_______________________________________________ >General Forum at Bioinformatics.Org - >BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From aloraine at gmail.com Sat Mar 24 16:07:25 2007 From: aloraine at gmail.com (Ann Loraine) Date: Sat, 24 Mar 2007 14:07:25 -0600 Subject: [BiO BB] refs for rates of segmental (or smaller) duplication? Message-ID: <83722dde0703241307h4ffd82cfv89653a6b3652d12c@mail.gmail.com> Dear all, I've been scanning articles in PubMed looking for a study that has generated some data on size distributions for duplicated segments in the human (or other) genomes. If you know of such a study, please let me know! I want to know if the following statement is true: "Smaller-sized duplications (<2 kb) vastly outnumber larger-sized duplications (>2kb, 3, kb, etc.) in the [insert species here] genome." So far I've been able to find some papers that defined segmental duplication sizes differently (2 kb versus 5 kb, and so on) but no single study that looked at varying sizes using the equivalent discovery criteria. Yours, Ann -- Ann Loraine, Assistant Professor Departments of Genetics, Biostatistics, Computer and Information Sciences Associate Scientist, Comprehensive Cancer Center University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From mheusel at gmail.com Fri Mar 23 18:38:55 2007 From: mheusel at gmail.com (Martin Heusel) Date: Fri, 23 Mar 2007 23:38:55 +0100 Subject: [BiO BB] how to build a prediction website In-Reply-To: References: <5632703b0703231221l26a0db9fn2d0b351d7fe871ab@mail.gmail.com> Message-ID: <6127fc200703231538i2f93329akaab11b6f0e13d218@mail.gmail.com> For a quick webserver setup with MySQL, Perl and PHP maybe XAMPP is worth a look: http://www.apachefriends.org/en/xampp.html regards Martin -- + http://ni.cs.tu-berlin.de/ + http://www.bioinf.jku.at/ From tdmlwilo at yahoo.com Sun Mar 25 05:51:21 2007 From: tdmlwilo at yahoo.com (Twaha Daudi) Date: Sun, 25 Mar 2007 02:51:21 -0700 (PDT) Subject: [BiO BB] In need of guidance Message-ID: <943960.16971.qm@web37105.mail.mud.yahoo.com> Dear all, Iam new here and interested to know bioinformaics.My plan after knowing it is to set up small bioinformatics centre in my current employer (medical research institution- africa)using open source software if it is possible.My background is in Electronics and Communication(BSc) and graduate of MSc in Computer Systems Engineering(2007).The problem I'm facing now is where to start and which area to start with?. or should I take a Master program in bioinformatics?.I will appliciate for your help Thanking in advance. /T --------------------------------- Don't get soaked. Take a quick peek at the forecast with theYahoo! Search weather shortcut. From dan.bolser at gmail.com Mon Mar 26 09:15:13 2007 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 26 Mar 2007 15:15:13 +0200 Subject: [BiO BB] In need of guidance In-Reply-To: <943960.16971.qm@web37105.mail.mud.yahoo.com> References: <943960.16971.qm@web37105.mail.mud.yahoo.com> Message-ID: <2c8757af0703260615u53da5ca8wc9e6b7f91e199017@mail.gmail.com> On 25/03/07, Twaha Daudi wrote: > Dear all, > Iam new here and interested to know bioinformaics.My plan after knowing it is to set up small bioinformatics centre in my current employer (medical research institution- africa)using open source software if it is possible.My background is in Electronics and Communication(BSc) and graduate of MSc in Computer Systems Engineering(2007).The problem I'm facing now is where to start and which area to start with?. or should I take a Master program in bioinformatics?.I will appliciate for your help My advice is to read lots of books in bioinformatics before making any further choices. You can find a list of books at the 'Bioinformatics.Org Bookstore', which is here; http://wiki.bioinformatics.org/Books and I am sure the list will be happy to discuss their favourite bioinformatics books with you if you ask. Also there are specific mailing lists for educators and discussion of education relatied issues. I am sure people on this list can point you to those other lists (or search around the website). Good luck! Dan. > Thanking in advance. > /T > > > --------------------------------- > Don't get soaked. Take a quick peek at the forecast > with theYahoo! Search weather shortcut. > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- hello From amonti at unich.it Mon Mar 26 05:24:41 2007 From: amonti at unich.it (Andrea Monti) Date: Mon, 26 Mar 2007 11:24:41 +0200 Subject: [BiO BB] In need of guidance In-Reply-To: <943960.16971.qm@web37105.mail.mud.yahoo.com> References: <943960.16971.qm@web37105.mail.mud.yahoo.com> Message-ID: <46079159.3030900@unich.it> Dear Twaha Daudi apart from the technicalities of specific softwares and areas of work, I might suggest you to lay your work on some fundamental basis: 1 - follow secure programming techniques. It is a fact that software DO fails and every effort should be made to keep bugs and crashes at the very minimum (including backups, for instance), 2 - try to use open file formats. This option gives you the possibility of preserving data while time is passing, having access to "old" information without need of using third parties applications (and, BTW, remaining "owner" of you own information.) 3 - track any design and development workaround and solution and, most important, avoid "shortcut" to solve software problem (this could affect in unpredictable way the reliability of results.) 4 - as soon as you can, use UNIX based operating systems and software (they are more secure and reliable). Best. a > My background is in Electronics and Communication(BSc) and graduate of MSc in Computer Systems Engineering(2007).The problem I'm facing now is where to start and which area to start with?. or should I take a Master program in bioinformatics?.I will appliciate for your help > Thanking in advance. > /T > > > --------------------------------- > Don't get soaked. Take a quick peek at the forecast > with theYahoo! Search weather shortcut. > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From risea at cecalc.ula.ve Mon Mar 26 16:11:17 2007 From: risea at cecalc.ula.ve (risea at cecalc.ula.ve) Date: Mon, 26 Mar 2007 16:11:17 -0400 (VET) Subject: [BiO BB] Bioinformatics 2007 - Spain Message-ID: <43294.150.185.138.49.1174939877.squirrel@mail.cecalc.ula.ve> Bioinformatics 2007 Torremolinos, M?laga (Spain) 11-14 June 2007 Workshop on Collaborative Bioinformatics EMBnet Annual General Meeting RIB Annual General Meeting An international workshop on collaborative Bioinformatics will be held in Torremolinos during 11 th -13 th of June 2007 in coordination with the Annual General Meetings of the European Molecular Biology Network (EMBnet) and the Iberoamerican Bioinformatics Network (RIB). The workshop will present major scientific endeavours in four main Bioinformatics areas, with specific emphasis on their collaborative aspects and on building up prospective ties and collaborations between the participants. You are invited to register and submit an abstract for a contributed a posible poster or maybe a talk. Deadline for registration and abstracts: April 15. WORKSHOP PROGRAM Starting on June, 11 th in the afternoon, specific sessions will take place addressing current advances and opportunities for collaboration in major areas, with a final, informal closing session being devoted to general analysis and discussion of the topics presented taking place in the afternoon of June 13th. * Computational genomics and evolution (sequence analysis, multiple alignment and evolution) * Structural bioinformatics (structural biology, 3D-modelling and docking and computer assisted drug design) * Databases and Systems biology *Training in Bioinformatics More information at http://rib.cecalc.ula.ve/evento_2007.html Regards Raul Isea by Organizing committees ----------------------------------------------- Raul Isea ----------------------------------------------- E-mail: risea at cecalc.ula.ve CeCalCULA ULA. http://www.cecalc.ula.ve/ Home Page: http://webdelprofesor.ula.ve/ciencias/risea Centro de Teleinformaci?n. Parque Tecnol?gico de M?rida. http: www.cptm.ula.ve Av. 4 Edif. General Masini, Av. 4 entre c/18 y 19,Piso 3 M?rida, 5101, Venezuela. FAX +58-(0)274-2525473. 2do Email: lrisea at yahoo.com ------------------------------------------------ From pfern at igc.gulbenkian.pt Mon Mar 26 17:26:11 2007 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Mon, 26 Mar 2007 22:26:11 +0100 Subject: [BiO BB] In need of guidance In-Reply-To: <2c8757af0703260615u53da5ca8wc9e6b7f91e199017@mail.gmail.com> References: <943960.16971.qm@web37105.mail.mud.yahoo.com> <2c8757af0703260615u53da5ca8wc9e6b7f91e199017@mail.gmail.com> Message-ID: <1174944371.46083a7303a9c@webmail.igc.gulbenkian.pt> Hello Twaha Bioinformatics is (or can be) huge... Providing unlimited services is unmanageable. I reckong that your first difficulty, besides getting basic knowledge in books, it to assess the needs of your institution. I think that you should relate to international structures and learns some of the how-to's and why don'ts from them. Take a couple of training courses somewhere you can travel to. I am an EE myself and I went through that some 16 years ago. I had to learn a lot more about Biochemistry and Molecular Biology, for example. I run a trainig course programme myself. http://gtpb.igc.gulbenkian.pt Where are you located in Africa? Portugal is cheap to travel to bur maybe I can inidicate people in Africa that can be at easier reach. Pedro -- Pedro Fernandes Centro Portugu?s de Bioinform?tica Instituto Gulbenkian de Ci?ncia Apartado 14 2781 OEIRAS PORTUGAL Quoting Dan Bolser : > On 25/03/07, Twaha Daudi wrote: > > Dear all, > > Iam new here and interested to know bioinformaics.My plan after knowing > it is to set up small bioinformatics centre in my current employer (medical > research institution- africa)using open source software if it is possible.My > background is in Electronics and Communication(BSc) and graduate of MSc in > Computer Systems Engineering(2007).The problem I'm facing now is where to > start and which area to start with?. or should I take a Master program in > bioinformatics?.I will appliciate for your help > > My advice is to read lots of books in bioinformatics before making any > further choices. > > You can find a list of books at the 'Bioinformatics.Org Bookstore', > which is here; > > http://wiki.bioinformatics.org/Books > > > and I am sure the list will be happy to discuss their favourite > bioinformatics books with you if you ask. Also there are specific > mailing lists for educators and discussion of education relatied > issues. I am sure people on this list can point you to those other > lists (or search around the website). > > Good luck! > > Dan. > > > > Thanking in advance. > > /T > > > > > > --------------------------------- > > Don't get soaked. Take a quick peek at the forecast > > with theYahoo! Search weather shortcut. > > _______________________________________________ > > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > -- > hello > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From lixue at iastate.edu Mon Mar 26 19:34:23 2007 From: lixue at iastate.edu (Li Xue) Date: Mon, 26 Mar 2007 18:34:23 -0500 Subject: [BiO BB] Weka exception: premature end of line Message-ID: <200703262334.l2QNYeSF018012@mailhub-4.iastate.edu> Hello all, I am calling weka using command line in Window XP. But I get the following error report: java.lang.Exception: Weka exception: premature end of line, read Token[EOL], line 19585 My perl command is like this and it works for a smaller dataset: system "java -mx1024m weka.classifiers.bayes.NaiveBayes -t $trainfile -T $testfile -p $probpos > $outputfile"; How can I fix that? Thank you. Xue, Li Bioinformatics and Computational Biology Program Iowa State University 1-515-5201676 From fireinthewind at gmail.com Thu Mar 29 10:09:57 2007 From: fireinthewind at gmail.com (Kim Clarke) Date: Thu, 29 Mar 2007 15:09:57 +0100 Subject: [BiO BB] php and seqret Message-ID: <33a85e2f0703290709t6081254cx5670dbfdd95b749b@mail.gmail.com> Hi folks, I'm a first year bioinformatics undergraduate nearing completion of my first year project. A quick question...I am writing a very simple web server using basic html and php. One section of the php deals with calling Seqret (EMBOSS) using exec(). Seqret is stored on the same file server and the command line instruction when ran in a terminal works fine. here is the snippet of code: //exec("touch $pass_c"); exec("seqret embl:$accession $pass_c"); both $accession and $pass_c work fine. Can anyone with experience of PHP and EMBOSS help me? is it a problem with file permissions? Kim From dpsdevi at gmail.com Fri Mar 30 11:45:26 2007 From: dpsdevi at gmail.com (Divya P Syamaladevi) Date: Fri, 30 Mar 2007 21:15:26 +0530 Subject: [BiO BB] download_Pfam Message-ID: <3af7110c0703300845h6c63a23cvf3ddc3f42e23a5f3@mail.gmail.com> hi all, I would like to download the domain architecture from pfam along with the taxonomic ids.Is there any single site from where one can download this? Many thanks in advance dpsdevi From divyaps at ncbs.res.in Fri Mar 30 14:17:37 2007 From: divyaps at ncbs.res.in (Divya P Syamala) Date: Fri, 30 Mar 2007 23:47:37 +0530 (IST) Subject: [BiO BB] pfam Message-ID: <33233.192.168.1.1.1175278657.squirrel@mail.ncbs.res.in> hi all, I have been trying to download some information from Pfam database.I couldn't figure out what the titles for the downloaded information from the following links are: ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/architecture.txt.gz ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/pfamA_architecture.txt.gz ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/pfamseq_architecture.txt.gz Secondly I would like to know how to get the taxonomy information for a list of genebank ids. Thanks in advance divya From dan.bolser at gmail.com Sat Mar 31 04:56:42 2007 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 31 Mar 2007 09:56:42 +0100 Subject: [BiO BB] pfam In-Reply-To: <33233.192.168.1.1.1175278657.squirrel@mail.ncbs.res.in> References: <33233.192.168.1.1.1175278657.squirrel@mail.ncbs.res.in> Message-ID: <2c8757af0703310156w3a3f5793y73bebf9ed6515028@mail.gmail.com> On 30/03/07, Divya P Syamala wrote: > hi all, > I have been trying to download some information from Pfam database.I > couldn't figure out what the titles for the downloaded information from > the following links are: Dude... did you read the README? It points to the following page; http://www.sanger.ac.uk/Software/Pfam/help/rdb_doc.shtml This doesn't directly give a list of column id's and descriptions but does give enough information for you to get going with the database. The columns (and files) should at least become easier to understand once you have read that page. > ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/architecture.txt.gz > ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/pfamA_architecture.txt.gz > ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/pfamseq_architecture.txt.gz > > Secondly I would like to know how to get the taxonomy information for a list > of genebank ids. If you read the above you will see that taxonomic information is included in the pfam database. However, to answer your question, you can get that data from here... Dang... things keep moving around! Or perhaps I just forgot... the file 'gi_taxid_nucl.dmp' is what you need and it is under here... ftp://ftp.ncbi.nih.gov/pub/taxonomy/ Google also shows a number of API services that serve up this mapping. > Thanks in advance > divya > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From idoerg at burnham.org Sat Mar 31 16:19:56 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat, 31 Mar 2007 13:19:56 -0700 Subject: [BiO BB] AFP - BioSapiens Joint SIG at ECCB 2007: first call for submissions Message-ID: <460EC26C.5060300@burnham.org> Joint AFP-Biosapiens SIG http://2007.BioFunctionPrediction.org The Automated Function Prediction (AFP) SIG and the Biosapiens European network of excellence in genome annotation are teaming up to hold a two-day Special Interest Group (SIG) meeting July 19-20, 2007 alongside ISMB/ECCB 2007. The abstract submission site is now open. Two page abstracts for posters or short talks will be accepted until May 1, 2007. Please go to: http://2007.BioFunctionPrediction.org/node/2 to submit your abstracts. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through to predicting the function from protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a SIG that will deal with a wide scope of gene, protein, and genomic annotations. Talks are sought in, but not limited to: * Various aspects of gene and protein function prediction o Function prediction using sequence based methods. This would include "classic" methods such as detection of functional motifs and inferring function from sequence similarity. o Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss. o Phylogeny based methods o Function from molecular interactions o Function from structure o Function prediction using combined methods o "Meta-talks" discussing the limitations and horizons of computational function prediction. o Assessing function prediction programs * Genomic annotation o Gene finding o Genome visualization o Collaborative annotation o Cooperation between experimental and computational biologists Confirmed speakers include: * Janet Thornton, European Bioinformatics Institute, Cambridge, UK * David Jones University College, London, UK * Rob Russell EMBL, Heidelberg, Germany * Christine Orengo, University College London, UK * Alfonso Valencia, Centro Nacional de Biotecnologia, Madrid, Spain * Ewan Birney, European Bioinformatics Institute, Cambridge, UK * Shoshana Wodak, University of Toronto, Canada * Russ Altman, Stanford University, USA Organizers: Iddo Friedberg, Burnham Institute for Medical Research, La Jolla, CA, USA Adam Godzik, Burnham Institute for Medical Research and University of California, San Diego Christine Orengo, University College, London Important dates: May 1 2007: Talk and poster abstracts due May 21 2007: notification of acceptance May 28, 2007: final abstracts due July 19-20, 2007: AFP-Biosapiens SIG alongside ISMB/ECCB 2007 in Vienna, Austria. Contact us: afp.biosap.2007 at gmail.com For more information: http://2007.BioFunctionPrediction.org -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 http://iddo-friedberg.org http://BioFunctionPrediction.org From esegura at vrlsoft.com Fri Mar 30 21:09:48 2007 From: esegura at vrlsoft.com (esegura at vrlsoft.com) Date: Fri, 30 Mar 2007 18:09:48 -0700 Subject: [BiO BB] CFP - 2nd IEEE International Workshop on Software Stability at Work (SSW 2007) Message-ID: <59de8442c6ccc42cdca2e6ee85c2a715@ijop.org> -- If you do not want to receive any more newsletters, http://ijop.org/mailing-lists/?p=unsubscribe&uid=d9236f128ee3a808142bce82f449a3e9 To update your preferences and to unsubscribe visit http://ijop.org/mailing-lists/?p=preferences&uid=d9236f128ee3a808142bce82f449a3e9 Forward a Message to Someone http://ijop.org/mailing-lists/?p=forward&uid=d9236f128ee3a808142bce82f449a3e9&mid=10 -- Powered by PHPlist, www.phplist.com -- From timmcilveen at talktalk.net Sat Mar 31 15:57:56 2007 From: timmcilveen at talktalk.net (Tim) Date: Sat, 31 Mar 2007 20:57:56 +0100 Subject: [BiO BB] mxtextools Message-ID: <1175371076.6587.3.camel@linux-eslv.site> Hi, I have installed Suse 10.2 linux on my computer which came packaged with Python 2.5. I notice on the mxtexttools website that their is only a tar file up to python 2.4 . Has anyone tried the 2.4 texttools with python 2.5. Is it compatible? Thanks, Tim