From pmr at ebi.ac.uk Wed Nov 1 06:51:51 2006 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 01 Nov 2006 11:51:51 +0000 Subject: [BiO BB] NJ distance matrix error (Phylip) In-Reply-To: <726450810610311358n11a01346x71f21c8d9e957c52@mail.gmail.com> References: <726450810610311358n11a01346x71f21c8d9e957c52@mail.gmail.com> Message-ID: <45488A57.2000508@ebi.ac.uk> Samantha Fox wrote: > Hi, > > I had a very simple question. The distance matrix I input to > Neighbor-Joining gives error for incorrect input file ! > > Here is the matrix > dmel 0 13 13 25 29 31 28 34 Tricky to find good documentation on this. I suggest one or more of the following, depending on what version of phylip (or another package) you are using to read the file. Missing header record (should say 12 on the line above the data) The ID is defined as 10 characters generally in phylip, so it may need a couple of extra spaces to save the ID being "dmel 0" The values are floating point so adding .0 after each one could be useful. Integers in these files are valid as "replicates" and would make some programs read the file as having only half the distance values on each line. Hope that helps, Peter Rice From dafniosn at post.tau.ac.il Wed Nov 1 04:46:43 2006 From: dafniosn at post.tau.ac.il (Osnat Dafni) Date: Wed, 1 Nov 2006 11:46:43 +0200 Subject: [BiO BB] Error messages when running blastpgp (NCBI PSI-BLAST) In-Reply-To: <4547A010.60201@burnham.org> References: <1162278163.4546f513af14e@webmail.tau.ac.il> <4547A010.60201@burnham.org> Message-ID: <1162374403.45486d03cde57@webmail.tau.ac.il> The database was downloaded as a fasta file, and I used NCBI's "formatdb" before running blastpgp. Unfortunately I don't have the exact command line used with formatdb, but I did not used any special options - everything was set to default. I have some hints that this is a memory issue: when I remove half the sequences from the input file, the errors go away, and when I decrease the value of parameters such as -e and -h (e-value cut-offs), I get less error lines. However, it still puzzles me why would changing the output format with -m (as I wrote in my previous message) eliminates the errors (or perhaps just reduces them for the input file size I'm using for my debugging). Quoting Iddo Friedberg : > Osnat Dafni wrote: > > need more info.. how did you formatdb your database? > > Iddo > > > Hi, > > > > I'm trying to run the local version of ncbi psi-blast (blastpgp) using a > > self-generated database and a fasta query file. I get the following error > > messages repeatedly while the program runs: > > > > [NULL_Caption] ERROR: ncbiapi [000.000] BioseqFindFunc: couldn't uncache > > [NULL_Caption] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed > with idx > > 2048 > > > > I'm using the following command line: > > > > blastpgp -d db_file -i query_file -e 1.0 -m 8 -o output_file -I T -a 2 -j 4 > -h > > 0.001 > > > > While experimenting I've noticed that when replacing the option "-m 8" > (tabular > > output format) with "-m 0" (default output format), the errors go away. > > > > Does any one has any information about what could be causing these errors? > > Thanks in advance. > > > > ---------------------------------------------------------------- > > This message was sent using IMP, the Internet Messaging Program. > > > > _______________________________________________ > > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > -- > > Iddo Friedberg, Ph.D. > Burnham Institute for Medical Research > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > Tel: (858) 646 3100 x3516 > Fax: (858) 795 5249 ** NEW ** > http://iddo-friedberg.org > http://BioFunctionPrediction.org > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > +++++++++++++++++++++++++++++++++++++++++++ > This Mail Was Scanned By Mail-seCure System > at the Tel-Aviv University CC. > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From skhadar at gmail.com Thu Nov 2 06:33:08 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 2 Nov 2006 03:33:08 -0800 Subject: [BiO BB] QSAR Values for Organic compounds Message-ID: Dear All, I am interested to know the QSAR values of a set of molecules in standard condition. Is there any web page / database available for QSAR values (or a dictionary of QSAR values ) of organic molecules including amino acids ? Cheers, -- Shameer Khadar -------------- next part -------------- An HTML attachment was scrubbed... URL: From bikash_lohia at yahoo.co.in Thu Nov 2 03:56:47 2006 From: bikash_lohia at yahoo.co.in (Bikash Lohia) Date: Thu, 2 Nov 2006 08:56:47 +0000 (GMT) Subject: [BiO BB] a query In-Reply-To: <20061019160100.6340F368631@primary.bioinformatics.org> Message-ID: <20061102085647.73449.qmail@web8813.mail.in.yahoo.com> what is the difference between Mega Blast and blast --------------------------------- Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW -------------- next part -------------- An HTML attachment was scrubbed... URL: From austin.tanney at almacgroup.com Thu Nov 2 09:11:24 2006 From: austin.tanney at almacgroup.com (Tanney, Austin) Date: Thu, 2 Nov 2006 14:11:24 -0000 Subject: [BiO BB] a query Message-ID: http://www.ncbi.nlm.nih.gov/blast/megablast.shtml -----Original Message----- From: bio_bulletin_board-bounces+austin.tanney=almacgroup.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+austin.tanney=almacgroup.com at bioinformatics.org]On Behalf Of Bikash Lohia Sent: 02 November 2006 08:57 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] a query what is the difference between Mega Blast and blast _____ Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW Proprietary or confidential information belonging to Almac Group Limited or to one of its affiliated companies may be contained in this message. The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at almacgroup.com and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioinfosm at gmail.com Thu Nov 2 17:04:32 2006 From: bioinfosm at gmail.com (Samantha Fox) Date: Thu, 2 Nov 2006 17:04:32 -0500 Subject: [BiO BB] NJ distance matrix error (Phylip) In-Reply-To: <45488A57.2000508@ebi.ac.uk> References: <726450810610311358n11a01346x71f21c8d9e957c52@mail.gmail.com> <45488A57.2000508@ebi.ac.uk> Message-ID: <726450810611021404ta1bb4c8kd7c731cf867ac16d@mail.gmail.com> wowww !! It was to do with length 10.. . I put in 2 extra spaces and it worked !! Such a popular and heavily used program having these kinds of errors ! Thanks for the help though :) ~S On 11/1/06, Peter Rice wrote: > > Samantha Fox wrote: > > Hi, > > > > I had a very simple question. The distance matrix I input to > > Neighbor-Joining gives error for incorrect input file ! > > > > Here is the matrix > > dmel 0 13 13 25 29 31 28 34 > > Tricky to find good documentation on this. > > I suggest one or more of the following, depending on what version of > phylip (or > another package) you are using to read the file. > > Missing header record (should say 12 on the line above the data) > > The ID is defined as 10 characters generally in phylip, so it may need a > couple > of extra spaces to save the ID being "dmel 0" > > The values are floating point so adding .0 after each one could be useful. > Integers in these files are valid as "replicates" and would make some > programs > read the file as having only half the distance values on each line. > > Hope that helps, > > Peter Rice > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Fri Nov 3 04:07:01 2006 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 3 Nov 2006 09:07:01 -0000 (GMT) Subject: [BiO BB] NJ distance matrix error (Phylip) In-Reply-To: <726450810611021404ta1bb4c8kd7c731cf867ac16d@mail.gmail.com> References: <726450810610311358n11a01346x71f21c8d9e957c52@mail.gmail.com> <45488A57.2000508@ebi.ac.uk> <726450810611021404ta1bb4c8kd7c731cf867ac16d@mail.gmail.com> Message-ID: <1607.217.44.133.216.1162544821.squirrel@webmail.ebi.ac.uk> Samantha Fox wrote: > wowww !! > It was to do with length 10.. . I put in 2 extra spaces and it worked !! > Such a popular and heavily used program having these kinds of errors ! "That's not a bug ... it's a feature" It was also a good test for the EMBOSS version of phylip which gave an error and still failed to decode the file. It has no ID length limit, but was tripped up by the integers and the missing header line. Phylip imposed the 10 character ID limit at a time when it was reasonable as all the major databases had a maximum of 9 and it reather got frozen. Removing it now would be sure to break someone else's data somewhere. Bioinformatics is full of such quirks. Glad it helped. Peter From sschuster at clcbio.com Fri Nov 3 06:23:05 2006 From: sschuster at clcbio.com (Stefan Schuster) Date: Fri, 03 Nov 2006 12:23:05 +0100 Subject: [BiO BB] Blast Output statistics - xml vs plain text Message-ID: <454B2699.4080601@clcbio.com> Hello, performing a blastx search against RefSeq using the NCBI webblast (details below), the statistics section of the text output contains amongst others following lines: Length of database: 926984281 Length adjustment: 36 Effective length of query: 157 Effective length of database: 834733201 Effective search space: 23372529628 Effective search space used: 23372529628 The statics section of the xml output for exactly the same search (same RID) contains amongst others follwing entries: 926984281 0 0 How can the difference between "Effective search space" in the text output and "Statistics_eff-space" int the xml output be explained? Which field in the xml output reffers to which field in the html output? Is there a detailed description for all values of the statistics section available? thanks in advance for helping Stefan details for blast query: RID: 1162550444-15189-25311546969.BLASTQ2 Programm: blastx database: refseq all other parameters have default settings. used query sequence: >testsequence1 CCGCCCGCCCGCCCGCAGGGACCACGCGCGGGGAAACCCGGAGCTGGCGCGGCTTCGTCC CGGGCTGGCGGTGCTGGGCGCGGACGAGCGCATCTTCTCGCTGACGCGCAGGCTGGCGCA CGGCGAGGAGCTGCGGGTGAGCGCGCGCTCCCGGGAGGGGCGGGGAGGGCGCCCCGGGTC CACCCGCCCTCAC From asidhu at biomap.org Sat Nov 4 06:07:34 2006 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Sat, 4 Nov 2006 22:07:34 +1100 (EST) Subject: [BiO BB] 3rd CFP: IEEE Workshop on Biomedical Applications for Digital Ecosystems (BADE 2007) Message-ID: <50552.144.136.103.129.1162638454.squirrel@biomap.org> 2007 IEEE Workshop on Biomedical Applications for Digital Ecosystems (BADE 2007) in conjunction with Inaugural IEEE International Digital Ecosystems and Technology Conference 2007 20 February 2007, Cairns, Australia http://bade07.biomap.org/ Scope of the workshop: The primary focus of BADE 2007 workshop is to share research applications using biomedical data and to identify new issues and directions for future research in biomedical applications. Authors are invited to submit original papers to the workshop exploring theories, techniques, and applications for biomedicine. Papers are invited, but not limited to the following themes: * Bioinformatics and Computational Biology * Data Representation and Visualization * Biological Databases & Data Integration * Microarray analysis * Protein and RNA structure prediction * Feature selection and pattern discovery in biological data * System Biology and Pathways * Biomedical Ontologies and taxonomies * Text Mining * Health Care Information Systems * Electronic Health Records * Clinical Assessment and Patient Diagnosis * Disease Control and Prevention * Privacy and Security in Healthcare Important Dates: * Submission of Full Papers: November 10, 2006 * Notification of Acceptance: December 10, 2006 * Camera-ready Copies of papers: December 31, 2006 Paper Submission Procedures: All paper submissions will be handled electronically at: http://bradleyuniversityvolunteer.ieee-ies.org/submit/dest07/ * Authors are Invited to submit electronically, a full paper (6 pages, about 4500 words, PDF file) of their original work. * Select "W01: Biomedical Applications" in Technical Track drop down menu on Author Page. High quality papers in biomedical applications are solicited. Original papers exploring new directions will receive especially careful and supportive reviews. Papers that have already been accepted or are currently under review for other conferences or journals will not be considered for publication at IEEE DEST 2007. Paper submissions should be in the IEEE 2-column format, and will be reviewed by the Program Committee on the basis of technical quality, relevance, originality, significance, and clarity. Accepted IEEE BADE 2007 will be published in the conference proceedings by IEEE Industrial Electronics Society and will be included in EI index and IEEE Xplore. General Chairs: Tharam S. Dillon (University of Technology Sydney, Australia) Elizabeth Chang (Curtin University of Technology, Australia) Program Chairs: Amandeep S. Sidhu (University of Technology Sydney, Australia) Xiaohua Hu (Drexel University, USA) Farookh Hussain (Curtin University of Technology, Australia) Maja Hadzic (Curtin University of Technology, Australia) For further inquiries, please contact bade07 at biomap.org -- Amandeep S. Sidhu, MIEEE, MACM, MAPBioNet Researcher (Bioinformatics) Room CB10.04.130 Faculty of Information Technology University of Technology, Sydney PO Box 123 Broadway, NSW 2007, Australia UTS Email: asidhu"AT SIGN"it.uts.edu.au Personal Email: asidhu"AT SIGN"biomap.org Personal Web: http://www.amandeep.org/ Project Web: http://www.proteinontology.info/ Ph: +61 2 9514 4469 Fax: +61 2 9514 1807 Mobile: +61 448897900 From Michael.Cox at liverpool.ac.uk Fri Nov 3 10:45:14 2006 From: Michael.Cox at liverpool.ac.uk (Cox, Mike) Date: Fri, 3 Nov 2006 15:45:14 -0000 Subject: [BiO BB] Hierarchical Probe Design Message-ID: Dear All, Was wondering whether anyone knew of a suitable program for preparing hierarchical groups of probes based on alignments of DNA, such as Hierarchical Probe Designer: Design of long oligonucleotide probes for functional gene detection in a microbial community; Chung et al.; Bioinformatics 2005 21(22):4092-4100 I would love to use this program, which is uses phylogenetic trees as a basis for probe design, but despite extensive searching, I can no longer find it. The URL quoted in the paper is no longer current. thanks very much for any help Mike Cox -------------------------------- Postdoctoral Research Associate Division of Genomics and Molecular Microbiology School of Biological Sciences University of Liverpool Crown Street Liverpool L69 7ZB Office 0151 7954576 Lab 0151 7954580 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hmbabu at gmail.com Mon Nov 6 02:18:02 2006 From: hmbabu at gmail.com (Babu H) Date: Mon, 6 Nov 2006 15:18:02 +0800 Subject: [BiO BB] information Message-ID: <73f8b4880611052318m7e99a345oabd5179e508ffafe@mail.gmail.com> Hi All where can i get the bioinformatics details/articles.. -------------- next part -------------- An HTML attachment was scrubbed... URL: From logan at cacs.louisiana.edu Mon Nov 6 10:35:04 2006 From: logan at cacs.louisiana.edu (Raja Loganantharaj) Date: Mon, 06 Nov 2006 09:35:04 -0600 Subject: [BiO BB] information In-Reply-To: <73f8b4880611052318m7e99a345oabd5179e508ffafe@mail.gmail.com> References: <73f8b4880611052318m7e99a345oabd5179e508ffafe@mail.gmail.com> Message-ID: <454F5628.7020602@cacs.louisiana.edu> please google with bioinformatics and get 26,900,000 hits. If you do not know what exactly you are looking for, it is hard to get anywhere from the number of hits. You may want to google bioinformatics overview or review articles to narrow down your search. good luck. Babu H wrote: > Hi All > > where can i get the bioinformatics details/articles.. > >------------------------------------------------------------------------ > >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gary at primary.bioinformatics.org Mon Nov 6 10:52:41 2006 From: gary at primary.bioinformatics.org (Gary Van Domselaar) Date: Mon, 6 Nov 2006 10:52:41 -0500 (EST) Subject: [BiO BB] information In-Reply-To: <454F5628.7020602@cacs.louisiana.edu> References: <73f8b4880611052318m7e99a345oabd5179e508ffafe@mail.gmail.com> <454F5628.7020602@cacs.louisiana.edu> Message-ID: try the bioinformatics.org FAQ: http://bioinformatics.org/faq On Mon, 6 Nov 2006, Raja Loganantharaj wrote: > please google with bioinformatics and get 26,900,000 hits. If you do not know > what exactly you are looking for, it is hard to get anywhere from the number > of hits. You may want to google bioinformatics overview or review articles to > narrow down your search. > > good luck. > > Babu H wrote: > >> Hi All >> where can i get the bioinformatics details/articles.. >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > -- Gary Van Domselaar, PhD Associate Director, Bioinformatics.Org gary at bioinformatics.org From zuofengli at yahoo.com Mon Nov 6 22:59:58 2006 From: zuofengli at yahoo.com (zuofeng li) Date: Mon, 6 Nov 2006 19:59:58 -0800 (PST) Subject: [BiO BB] Hierarchical Probe Design In-Reply-To: Message-ID: <20061107035958.57057.qmail@web51111.mail.yahoo.com> Dear sir: The url quoted in the paper is out of service. However, I get the HPD by following url. http://brcapp.kribb.re.kr/. Good luck! Zuofeng li SCBIT in China. --- "Cox, Mike" wrote: > Dear All, > > Was wondering whether anyone knew of a suitable > program for preparing hierarchical groups of probes > based on alignments of DNA, such as Hierarchical > Probe Designer: > > Design of long oligonucleotide probes for functional > gene detection in a microbial community; Chung et > al.; Bioinformatics 2005 21(22):4092-4100 > > I would love to use this program, which is uses > phylogenetic trees as a basis for probe design, but > despite extensive searching, I can no longer find > it. The URL quoted in the paper is no longer > current. > > thanks very much for any help > > Mike Cox > > -------------------------------- > Postdoctoral Research Associate > Division of Genomics and Molecular Microbiology > School of Biological Sciences > University of Liverpool > Crown Street > Liverpool > L69 7ZB > > Office 0151 7954576 > Lab 0151 7954580 > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ____________________________________________________________________________________ Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com From Alex.Bossers at wur.nl Tue Nov 7 02:13:32 2006 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Tue, 7 Nov 2006 08:13:32 +0100 Subject: [BiO BB] Hierarchical Probe Design In-Reply-To: Message-ID: <47C53C762312C548BF23B6556377B3EB213195@scomp0038.wurnet.nl> Hi Try this. It's the HPD you are looking for. http://brcapp.kribb.re.kr/ Alex ________________________________ Van: bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.org [mailto:bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.or g] Namens Cox, Mike Verzonden: vrijdag 3 november 2006 16:45 Aan: BiO_Bulletin_Board at bioinformatics.org Onderwerp: [BiO BB] Hierarchical Probe Design Dear All, Was wondering whether anyone knew of a suitable program for preparing hierarchical groups of probes based on alignments of DNA, such as Hierarchical Probe Designer: Design of long oligonucleotide probes for functional gene detection in a microbial community; Chung et al.; Bioinformatics 2005 21(22):4092-4100 I would love to use this program, which is uses phylogenetic trees as a basis for probe design, but despite extensive searching, I can no longer find it. The URL quoted in the paper is no longer current. thanks very much for any help Mike Cox -------------------------------- Postdoctoral Research Associate Division of Genomics and Molecular Microbiology School of Biological Sciences University of Liverpool Crown Street Liverpool L69 7ZB Office 0151 7954576 Lab 0151 7954580 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ahmed at pobox.com Tue Nov 7 10:07:51 2006 From: ahmed at pobox.com (Ahmed Moustafa) Date: Tue, 07 Nov 2006 09:07:51 -0600 Subject: [BiO BB] API for gene ontology retrieval? Message-ID: <4550A147.5060603@pobox.com> Hi All, Is there some API or an automated method to retrieve the annotation (gene ontology?) of a set of sequences? I believe BLAST is necessary but after BLASTing the sequences, how can I get the annotations (e.g. cellular component, pathway, biological function...) of (for example) the best hit for each sequence? Your help will be appreciated so much! Thanks in advance, Ahmed From skhadar at gmail.com Wed Nov 8 00:59:52 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 8 Nov 2006 11:29:52 +0530 Subject: [BiO BB] API for gene ontology retrieval? In-Reply-To: <4550A147.5060603@pobox.com> References: <4550A147.5060603@pobox.com> Message-ID: Try here : http://www.geneontology.org/GO.tools.shtml On 11/7/06, Ahmed Moustafa wrote: > > Hi All, > Is there some API or an automated method to retrieve the annotation > (gene ontology?) of a set of sequences? > I believe BLAST is necessary but after BLASTing the sequences, how can I > get the annotations (e.g. cellular component, pathway, biological > function...) of (for example) the best hit for each sequence? > Your help will be appreciated so much! > Thanks in advance, > Ahmed > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From insight.robin at gmail.com Tue Nov 7 20:43:10 2006 From: insight.robin at gmail.com (Rob C) Date: Tue, 7 Nov 2006 20:43:10 -0500 Subject: [BiO BB] API for gene ontology retrieval? In-Reply-To: <4550A147.5060603@pobox.com> References: <4550A147.5060603@pobox.com> Message-ID: If performance is not a consideration, you may try irobotsoft from http://irobotsoft.com. It has a visual interface for programming web robots, and also has an ActiveX interface for programmers. They have an example 'blastx.irb' for the blast search automation. Yours, rob On 11/7/06, Ahmed Moustafa wrote: > > Hi All, > Is there some API or an automated method to retrieve the annotation > (gene ontology?) of a set of sequences? > I believe BLAST is necessary but after BLASTing the sequences, how can I > get the annotations (e.g. cellular component, pathway, biological > function...) of (for example) the best hit for each sequence? > Your help will be appreciated so much! > Thanks in advance, > Ahmed > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nchandra at physics.iisc.ernet.in Wed Nov 8 01:24:37 2006 From: nchandra at physics.iisc.ernet.in (Dr.Nagasuma Chandra) Date: Wed, 8 Nov 2006 11:54:37 +0530 (IST) Subject: [BiO BB] CIBS06- computational insights into biological systems, IISc, Bangalore In-Reply-To: References: Message-ID: Call for Abstracts CIBS06- COMPUTATIONAL INSIGHTS INTO BIOLOGICAL SYSTEMS 26th to 28th December, 2006, Indian Institute of Science, Bangalore, India http://www.serc.iisc.ernet.in/~cibs06/ CIBS06 - is a satellite meeting of InCoB 2006 (INternational COnference on Bioinformatics, http://www.incob2006.in). The meeting focuses on various areas of biological networks and systems biology in general. Areas of Interest: * Network Biology * Structural Bioinformatics * Genome Analysis * Microarray Informatics * Systems and Synthetic Biology * Machine Learning Methods * Mathematical Modelling * Pathway Analysis * in silico methods in drug discovery The meeting will have talks from leading scientists from across the globe in many of these areas. The meeting will also have discussion sessions on selected topics, providing a forum to discuss new concepts and methodologies and any major concerns of wide interest to the community. Meeting deadlines: Abstract Submission 21st November 2006 Notification of Acceptance 30th November 2006 Registration Now open; closes on 7th December 2006 Abstracts submitted may be considered for poster or oral presentations. Conference flyer: http://www.serc.iisc.ernet.in/~cibs06/flyer.jpg E-mail: cibs06 at serc.iisc.ernet.in -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From erant at psb.ugent.be Wed Nov 8 05:18:29 2006 From: erant at psb.ugent.be (Erick Antezana) Date: Wed, 08 Nov 2006 11:18:29 +0100 Subject: [BiO BB] API for gene ontology retrieval? In-Reply-To: <4550A147.5060603@pobox.com> References: <4550A147.5060603@pobox.com> Message-ID: <4551AEF5.60801@psb.ugent.be> Hi Ahmed, the next release of the onto-perl suite will provide this functionality (still fixing the obo2owl conversion). We're also developing a web page for providing this service. Keep tuned... Check out http://www.cellcycleontology.org In principle, the API is for any OBO ontology (like GO, and of course CCO). Cheers, erick Ahmed Moustafa wrote: > Hi All, > Is there some API or an automated method to retrieve the annotation > (gene ontology?) of a set of sequences? > I believe BLAST is necessary but after BLASTing the sequences, how can > I get the annotations (e.g. cellular component, pathway, biological > function...) of (for example) the best hit for each sequence? > Your help will be appreciated so much! > Thanks in advance, > Ahmed > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- ================================================================== Erick Antezana Tel: 32 (0) 9 3313824 DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:erant at psb.ugent.be http://www.psb.ugent.be ================================================================== From cjm at fruitfly.org Fri Nov 10 01:22:48 2006 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 9 Nov 2006 22:22:48 -0800 Subject: [BiO BB] API for gene ontology retrieval? In-Reply-To: References: <4550A147.5060603@pobox.com> Message-ID: <0B29FE0D-6679-4C5A-B2A3-7EAFC11C421E@fruitfly.org> You can download the GO MySQL database and access it using the go-db- perl API. This assumes you already have identifiers for your best hits, and those identifiers have annotations associated with them. At this time the API does no perform any kind of enrichment analysis; if you want to do this sort of thing have a look at some of the tools on the GO website. There is no web service programmatic access for the database right now - you have to download it and access it that way. We'll hopefully have some kind of web service available soon, perhaps a SPARQL endpoint. Details for the API can be found here: http://www.godatabase.org/dev On Nov 7, 2006, at 5:43 PM, Rob C wrote: > If performance is not a consideration, you may try irobotsoft from > http://irobotsoft.com. > It has a visual interface for programming web robots, and also has > an ActiveX interface > for programmers. > > They have an example 'blastx.irb' for the blast search automation. > > Yours, > rob > On 11/7/06, Ahmed Moustafa wrote: Hi All, > Is there some API or an automated method to retrieve the annotation > (gene ontology?) of a set of sequences? > I believe BLAST is necessary but after BLASTing the sequences, how > can I > get the annotations (e.g. cellular component, pathway, biological > function...) of (for example) the best hit for each sequence? > Your help will be appreciated so much! > Thanks in advance, > Ahmed > > _______________________________________________ > 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 From karthik at rishi.serc.iisc.ernet.in Fri Nov 10 01:11:44 2006 From: karthik at rishi.serc.iisc.ernet.in (Karthik Raman) Date: Fri, 10 Nov 2006 11:41:44 +0530 Subject: [BiO BB] Domain Sequences Message-ID: Hello I was just wondering if it is possible to download the domain details for individual proteins of an organism. It would be useful to have the domain details either in terms of the accession number and the span (start and end letters in the sequence) or better still as faa files giving individual domain sequence. Is it possible to retrieve this from databases such as Pfam or InterPro? Any pointers? Regards Karthik -- ************************************************************************************** KARTHIK RAMAN Graduate Research Student Supercomputer Education and Research Centre/Bioinformatics Centre Indian Institute of Science, Bangalore Phone: +91-80-23601409/22932469 (Ext 24) Mobile: +91-98862-22404 Webpage: http://openwetware.org/wiki/Karthik_Raman Blog: http://karthikr.wordpress.com/ ************************************************************************************** From skhadar at gmail.com Fri Nov 10 09:46:06 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Fri, 10 Nov 2006 20:16:06 +0530 Subject: [BiO BB] Domain Sequences In-Reply-To: References: Message-ID: Hi, You have two option either you can download swissspfam from Pfam ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/swisspfam.gz or go to PRODOC - http://hodgkin.mbu.iisc.ernet.in/~prodoc/ and retreive domain assignments using the Pfam code. Trust this help. Shameer Khadar Jr. Research Fellow Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) On 11/10/06, Karthik Raman wrote: > > Hello > > I was just wondering if it is possible to download the domain details > for individual proteins of an organism. > > It would be useful to have the domain details either in terms of the > accession number and the span (start and end letters in the sequence) > or better still as faa files giving individual domain sequence. Is it > possible to retrieve this from databases such as Pfam or InterPro? > > Any pointers? > > Regards > Karthik > > -- > > ************************************************************************************** > KARTHIK RAMAN > Graduate Research Student > Supercomputer Education and Research Centre/Bioinformatics Centre > Indian Institute of Science, Bangalore > > Phone: +91-80-23601409/22932469 (Ext 24) > Mobile: +91-98862-22404 > Webpage: http://openwetware.org/wiki/Karthik_Raman > Blog: http://karthikr.wordpress.com/ > > ************************************************************************************** > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ahmed at pobox.com Fri Nov 10 19:28:55 2006 From: ahmed at pobox.com (Ahmed Moustafa) Date: Fri, 10 Nov 2006 18:28:55 -0600 Subject: [BiO BB] API for gene ontology retrieval? In-Reply-To: <0B29FE0D-6679-4C5A-B2A3-7EAFC11C421E@fruitfly.org> References: <4550A147.5060603@pobox.com> <0B29FE0D-6679-4C5A-B2A3-7EAFC11C421E@fruitfly.org> Message-ID: <45551947.4020106@pobox.com> Thank you all so much for your replies!!! I think Chri's approach, to download the database and deal with it, is the way to go. Do you know whether the GO database holds beyond the models organisms? Or would I have to restrict the BLAST search to a model organism to be able to retrieve the gene ontology later from the GO database for the hit? BTW, is there a plan to make the GO database remotely accessible (e.g. Ensembl core database)? Once again, thank you so much! Ahmed On 11/10/2006 12:22 AM, Chris Mungall wrote: > > You can download the GO MySQL database and access it using the go-db- > perl API. This assumes you already have identifiers for your best > hits, and those identifiers have annotations associated with them. At > this time the API does no perform any kind of enrichment analysis; if > you want to do this sort of thing have a look at some of the tools on > the GO website. > > There is no web service programmatic access for the database right > now - you have to download it and access it that way. We'll hopefully > have some kind of web service available soon, perhaps a SPARQL endpoint. > > Details for the API can be found here: > http://www.godatabase.org/dev > > On Nov 7, 2006, at 5:43 PM, Rob C wrote: > >> If performance is not a consideration, you may try irobotsoft from >> http://irobotsoft.com. >> It has a visual interface for programming web robots, and also has >> an ActiveX interface >> for programmers. >> >> They have an example 'blastx.irb' for the blast search automation. >> >> Yours, >> rob >> On 11/7/06, Ahmed Moustafa wrote: Hi All, >> Is there some API or an automated method to retrieve the annotation >> (gene ontology?) of a set of sequences? >> I believe BLAST is necessary but after BLASTing the sequences, how >> can I >> get the annotations (e.g. cellular component, pathway, biological >> function...) of (for example) the best hit for each sequence? >> Your help will be appreciated so much! >> Thanks in advance, >> Ahmed > From tejalonline at gmail.com Sun Nov 12 09:42:33 2006 From: tejalonline at gmail.com (T Joshi) Date: Sun, 12 Nov 2006 15:42:33 +0100 Subject: [BiO BB] Guidance Intended Message-ID: <11417a880611120642rcef8ef5ue7f76f96c67b73f5@mail.gmail.com> Hi ! I am a student and a beginner in Bioinformatics field. I want to do a project wherein I can find gene expressions for specific protein (or protein function) from the microarray data of various organisms. The problem is where I can find the microarray data of Yeast and other organisms? Please guide me. thanks in advance. Tejal From Stan.Gaj at BIGCAT.unimaas.nl Sun Nov 12 17:51:33 2006 From: Stan.Gaj at BIGCAT.unimaas.nl (Gaj Stan (BIGCAT)) Date: Sun, 12 Nov 2006 23:51:33 +0100 Subject: [BiO BB] Guidance Intended References: <11417a880611120642rcef8ef5ue7f76f96c67b73f5@mail.gmail.com> Message-ID: <1C6586068DF1054DA3899159C38B32C9315A59@um-mail0136.unimaas.nl> Hi Tejal, Usually Gene Expression Omnibus (GEO - http://www.ncbi.nlm.nih.gov/geo/) is a good place to start your search. This repository holds gene expression data for multiple microarray platforms and for multiple organisms as well. On a more personal note, I noticed that the raw data (numerical data you get after you scan your microarray plate) is for most arrays not available (although it ought to be!). So usually you'll stumble across genelists with only one column of numerical data, containing corrected (normalized) data. Be aware of this. Happy gene hunting! Stan -----Original Message----- From: bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinformatics.org on behalf of T Joshi Sent: Sun 12/11/2006 15:42 To: bbb at bioinformatics.org; bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Guidance Intended Hi ! I am a student and a beginner in Bioinformatics field. I want to do a project wherein I can find gene expressions for specific protein (or protein function) from the microarray data of various organisms. The problem is where I can find the microarray data of Yeast and other organisms? Please guide me. thanks in advance. Tejal _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From hsafer at alum.mit.edu Wed Nov 15 03:18:15 2006 From: hsafer at alum.mit.edu (Hershel Safer) Date: Wed, 15 Nov 2006 10:18:15 +0200 Subject: [BiO BB] ECCB early-registration deadline is this coming Tuesday! Message-ID: <455ACD47.7060001@alum.mit.edu> Save big by registering for the 5th European Conference on Computational Biology (ECCB '06) by November 21st! The early-registration deadline is only one week away, so register now. 5th European Conference on Computational Biology - ECCB ?'06 January 21-24, 2007 Eilat, Israel www.eccb06.org ** Registration: http://www.eccb06.org/new_pages/registration/registration.html ** Keynote speakers: http://www.eccb06.org/new_pages/program/program_keynote.html Prof. Naama Barkai, Weizmann Institute of Science Prof. Sir Tom Blundell, FRS, University of Cambridge Prof. Richard Karp, University of California, Berkeley Prof. Jeffrey Skolnick, Georgia Institute of Technology Prof. Marc Vidal, Harvard Medical School Prof. Martin Vingron, Max Planck Institute for Molecular Genetics ** Contributed papers: http://www.eccb06.org/new_pages/program/program_papers.html Now including late-breaking papers! ** Workshops: http://www.eccb06.org/new_pages/program/program_workshops.html ** Tutorials: http://www.eccb06.org/new_pages/program/program_tutorials.html ** Software demos: http://www.eccb06.org/new_pages/program/program_demos.html ** Posters: http://www.eccb06.org/new_pages/program/program_posters.html ** Help us spread the word -- Tell your friends to register with you!! ** For further information: See the conference website, http://www.eccb06.org , or send e-mail to the conference secretariat at eccb06 at diesenhaus.com. From mkgovindis at yahoo.com Mon Nov 13 22:35:08 2006 From: mkgovindis at yahoo.com (govind mk) Date: Mon, 13 Nov 2006 19:35:08 -0800 (PST) Subject: [BiO BB] Guidance Intended Message-ID: <20061114033508.88289.qmail@web34403.mail.mud.yahoo.com> Hi all, I was just wondering if there are any open source GEO file parsers (Bioperl/Biojava....) that can be used to parse the GEO soft format files. Regards Govind ----- Original Message ---- From: Gaj Stan (BIGCAT) To: bio_bulletin_board at bioinformatics.org Sent: Monday, November 13, 2006 4:21:33 AM Subject: Re: [BiO BB] Guidance Intended Hi Tejal, Usually Gene Expression Omnibus (GEO - http://www.ncbi.nlm.nih.gov/geo/) is a good place to start your search. This repository holds gene expression data for multiple microarray platforms and for multiple organisms as well. On a more personal note, I noticed that the raw data (numerical data you get after you scan your microarray plate) is for most arrays not available (although it ought to be!). So usually you'll stumble across genelists with only one column of numerical data, containing corrected (normalized) data. Be aware of this. Happy gene hunting! Stan -----Original Message----- From: bio_bulletin_board-bounces+stan.gaj=bigcat.unimaas.nl at bioinformatics.org on behalf of T Joshi Sent: Sun 12/11/2006 15:42 To: bbb at bioinformatics.org; bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Guidance Intended Hi ! I am a student and a beginner in Bioinformatics field. I want to do a project wherein I can find gene expressions for specific protein (or protein function) from the microarray data of various organisms. The problem is where I can find the microarray data of Yeast and other organisms? Please guide me. thanks in advance. Tejal _______________________________________________ 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 From kannaiah at bsd.uchicago.edu Tue Nov 14 13:32:36 2006 From: kannaiah at bsd.uchicago.edu (kannaiah at bsd.uchicago.edu) Date: Tue, 14 Nov 2006 12:32:36 -0600 Subject: [BiO BB] InterProscan XML output error Message-ID: <1163529156.455a0bc409e46@netmail.bsd.uchicago.edu> Hello, Anybody here use Interproscan anytime? If so, I am wondering if you ever ran into an error like this: An xml output error. Not sure whats going wrong here:(. Any ideas? Thank you. ----------------------------------------------------- [root at cccluster iprscan]# /clusta/shah/local_progs/iprscan/bin/iprscan -cli -appl hmmsmart -appl hmmpfam -i /clusta/shah/local_progs/iprscan/test.seq -o /clusta/shah/local_progs/iprscan/test.out SUBMITTED iprscan-20061114-12101842 FAILED Iprscan job iprscan-20061114-12101842 failed and exit with status code 256 /clusta/shah/local_progs/iprscan/bin/iprscan: /clusta/shah/local_progs/iprscan/tmp/20061114/iprscan-20061114-12101842/iprscan-20061114-12101842.xml unavailable : No such file or directory /clusta/shah/local_progs/iprscan/bin/iprscan_wrapper.pl: failed to send error to administrator: no destination address Tool: iprscan JobID: iprscan-20061114-12101842 Time: Tue Nov 14 12:11:37 2006 Error: supervise: doRawResults: failed to create XML output : Job submission parameters: DD 14 MM 11 YYYY 2006 appl hmmsmart,hmmpfam cmd submit crc 1 format xml frame 6 hh 12 jobid iprscan-20061114-12101842 mm 10 nseqs 3 onego 1 remotehost cccluster.uchicago.cc seq.1.1.crc64 F94D07049A6D489D seq.1.1.id RS16_ECOLI seq.1.1.len 82 seq.1.2.crc64 D44DAE8C544CB7C1 seq.1.2.id Q9RHD9 seq.1.2.len 267 seq.1.3.crc64 CD84A335CCFFE6D7 seq.1.3.id Y902_MYCTU seq.1.3.len 446 seqtype P srchtype interactive ss 18 submission cli tool iprscan NOTE: the newlines have been replaced with backslash. ---------------------------------------------------------- ------------------------------------------------- This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. ------------------------------------------------- From ulimard at yahoo.com.br Wed Nov 15 07:41:13 2006 From: ulimard at yahoo.com.br (Ulisses Dias) Date: Wed, 15 Nov 2006 12:41:13 +0000 (GMT) Subject: [BiO BB] Gene ontology PDB files In-Reply-To: <45551947.4020106@pobox.com> Message-ID: <20061115124114.10256.qmail@web56613.mail.re3.yahoo.com> Hi! Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term? Thank you Ulisses Dias __________________________________________________ Fale com seus amigos de gra?a com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ From skhadar at gmail.com Thu Nov 16 03:18:29 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 16 Nov 2006 13:48:29 +0530 Subject: [BiO BB] Gene ontology PDB files In-Reply-To: <20061115124114.10256.qmail@web56613.mail.re3.yahoo.com> References: <45551947.4020106@pobox.com> <20061115124114.10256.qmail@web56613.mail.re3.yahoo.com> Message-ID: Hi, You can get go id(s) for a PDB ID from PDB. I dont know about the reverse - better contact info at rcsb.org or info at pdb.org -- cheers On 11/15/06, Ulisses Dias wrote: > > Hi! > > Anyone knows how can I get the PDB numbers for all the genes products > associated to a GO term? > > Thank you > Ulisses Dias > > > > __________________________________________________ > 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 > From christoph.gille at charite.de Thu Nov 16 04:09:47 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 16 Nov 2006 10:09:47 +0100 (CET) Subject: [BiO BB] line wrap In-Reply-To: <200611152140.kAFLepli003832@smtp-vbr10.xs4all.nl> References: <200611152140.kAFLepli003832@smtp-vbr10.xs4all.nl> Message-ID: <41302.141.42.56.114.1163668187.squirrel@webmail.charite.de> Hello everyone, BiO_Bulletin_Board at bioinformatics.org do you know whether there is a standard short cut key to switch between line-wrap-mode and non-line-wrap-mode in text views / text editors in Bio applications ? I had been told that Visual Studio is using ctrl-D. So I checked Wordpad but it does not understand ctrl-D. What short cut key would you use ? From dgw106 at york.ac.uk Thu Nov 16 08:34:39 2006 From: dgw106 at york.ac.uk (DGW) Date: Thu, 16 Nov 2006 13:34:39 +0000 Subject: [BiO BB] Gene ontology PDB files In-Reply-To: <20061115124114.10256.qmail@web56613.mail.re3.yahoo.com> References: <20061115124114.10256.qmail@web56613.mail.re3.yahoo.com> Message-ID: <455C68EF.4000702@york.ac.uk> Hi, You can search/browse the PDB by GO term from this URL http://www.rcsb.org/pdb/static.do?p=search/index.html. You may need to have popups enabled on your browser. For example, I can click on Browse Database then Molecular Function and I get a tree of function categories on the right that I can expand by clicking on the arrows. Following 'binding' then 'nucleic acid binding', I click on RNA binding (GO ID:3723) and get 537 structures. The PDB IDs can be pulled out by using the options under Tabulate. You may need to know the hierarchy of the GO terms you are interested, e.g. from AmiGO, as it doesn't appear to be easy to search directly for the term of interest at the PDB site. Also, you are not guaranteed to find everything of interest - I think the PDB only considers a subset of all the available GO terms and even then not all PDB entries have GO terms assigned to them. If you need to be more comprehensive you might have to BLAST all your gene products against the PDB. Hope this helps! David Ulisses Dias wrote: > Hi! > > Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term? > > Thank you > Ulisses Dias > > > > __________________________________________________ > 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 > From cjm at fruitfly.org Thu Nov 16 18:51:10 2006 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 16 Nov 2006 15:51:10 -0800 Subject: [BiO BB] API for gene ontology retrieval? In-Reply-To: <45551947.4020106@pobox.com> References: <4550A147.5060603@pobox.com> <0B29FE0D-6679-4C5A-B2A3-7EAFC11C421E@fruitfly.org> <45551947.4020106@pobox.com> Message-ID: <481E78AA-E035-4EA7-A39C-3EB1B44376BA@fruitfly.org> On Nov 10, 2006, at 4:28 PM, Ahmed Moustafa wrote: > Thank you all so much for your replies!!! > I think Chri's approach, to download the database and deal with it, > is the way to go. > Do you know whether the GO database holds beyond the models organisms? Yes. > Or would I have to restrict the BLAST search to a model organism to > be able to retrieve the gene ontology later from the GO database > for the hit? I don't think so. But not every hit in your blast would correspond to something annotated with GO; and even if it did you probably have to deal with ID mapping somewhere. > BTW, is there a plan to make the GO database remotely accessible > (e.g. Ensembl core database)? Do you mean permit mysql access remotely, or provide some kind of REST-based API? When I looked into the former, there appeared to be a lack of good ways to throttle potential killer queries. For the latter we have nothing as yet, but should have something soon. > Once again, thank you so much! > Ahmed > > On 11/10/2006 12:22 AM, Chris Mungall wrote: > >> >> You can download the GO MySQL database and access it using the go- >> db- perl API. This assumes you already have identifiers for your >> best hits, and those identifiers have annotations associated with >> them. At this time the API does no perform any kind of enrichment >> analysis; if you want to do this sort of thing have a look at >> some of the tools on the GO website. >> >> There is no web service programmatic access for the database >> right now - you have to download it and access it that way. We'll >> hopefully have some kind of web service available soon, perhaps a >> SPARQL endpoint. >> >> Details for the API can be found here: >> http://www.godatabase.org/dev >> >> On Nov 7, 2006, at 5:43 PM, Rob C wrote: >> >>> If performance is not a consideration, you may try irobotsoft >>> from http://irobotsoft.com. >>> It has a visual interface for programming web robots, and also >>> has an ActiveX interface >>> for programmers. >>> >>> They have an example 'blastx.irb' for the blast search automation. >>> >>> Yours, >>> rob >>> On 11/7/06, Ahmed Moustafa wrote: Hi All, >>> Is there some API or an automated method to retrieve the annotation >>> (gene ontology?) of a set of sequences? >>> I believe BLAST is necessary but after BLASTing the sequences, >>> how can I >>> get the annotations (e.g. cellular component, pathway, biological >>> function...) of (for example) the best hit for each sequence? >>> Your help will be appreciated so much! >>> Thanks in advance, >>> Ahmed >> > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dgw106 at york.ac.uk Sat Nov 18 09:54:48 2006 From: dgw106 at york.ac.uk (David G Waterman) Date: Sat, 18 Nov 2006 14:54:48 +0000 Subject: [BiO BB] Ferguson plots Message-ID: <455F1EB8.5030803@york.ac.uk> Hi everyone, Does anyone know of a program for the PC that is capable of analysing gel electrophoresis data, in the form of relative mobilities, to generate a Ferguson plot? I found the Elphofit software via Google, but only managed to locate a Mac version, and I don't have access to a Mac at the moment. I've been using a spreadsheet to make the plot so far, but I think I could benefit from the analyses that a progam specific for the task may provide. Cheers, David From pjain at xldb.di.fc.ul.pt Thu Nov 16 04:54:09 2006 From: pjain at xldb.di.fc.ul.pt (Pooja Jain) Date: Thu, 16 Nov 2006 09:54:09 +0000 Subject: [BiO BB] Gene ontology PDB files In-Reply-To: References: <45551947.4020106@pobox.com> <20061115124114.10256.qmail@web56613.mail.re3.yahoo.com> Message-ID: <1163670849.455c3541870b2@webservices.di.fc.ul.pt> Hi, May be this is what you are looking for: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/gene_association.goa_pdb.gz Further Information about above file can be read from : ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/README An alternative option could be from PDB website. Please follow the link below: http://www.rcsb.org/pdb/static.do?p=search/index.html HTH -Pooja Quoting Shameer Khadar : > Hi, > You can get go id(s) for a PDB ID from PDB. > I dont know about the reverse - better contact info at rcsb.org or > info at pdb.org > -- > cheers > > > On 11/15/06, Ulisses Dias wrote: > > > > Hi! > > > > Anyone knows how can I get the PDB numbers for all the genes products > > associated to a GO term? > > > > Thank you > > Ulisses Dias > > > > > > > > __________________________________________________ > > 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 > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > --------------------------------------- Ms. Pooja Jain Ph.D. Student. Department of Physical Chemistry. School of Chemistry, University of Nottingham University Park Campus, NG7 2RD Cell: +44 7877 462595 Email: pcxpj1 at nottingham.ac.uk From nmulder at science.uct.ac.za Thu Nov 16 12:28:32 2006 From: nmulder at science.uct.ac.za (Dr Nicky Mulder) Date: Thu, 16 Nov 2006 17:28:32 +0000 Subject: [BiO BB] Re: Gene ontology PDB files & InterproScan query In-Reply-To: <20061116170129.9D18E368ACB@primary.bioinformatics.org> References: <20061116170129.9D18E368ACB@primary.bioinformatics.org> Message-ID: <455C9FC0.9050403@science.uct.ac.za> > > >------------------------------ > >Message: 3 >Date: Tue, 14 Nov 2006 12:32:36 -0600 >From: kannaiah at bsd.uchicago.edu >Subject: [BiO BB] InterProscan XML output error >To: bio_bulletin_board at bioinformatics.org >Message-ID: <1163529156.455a0bc409e46 at netmail.bsd.uchicago.edu> >Content-Type: text/plain; charset=ISO-8859-1 > >Hello, > >Anybody here use Interproscan anytime? >If so, I am wondering if you ever ran into an error like this: An xml output error. > >Not sure whats going wrong here:(. Any ideas? > >Thank you. > >----------------------------------------------------- >[root at cccluster iprscan]# /clusta/shah/local_progs/iprscan/bin/iprscan -cli >-appl hmmsmart -appl hmmpfam -i /clusta/shah/local_progs/iprscan/test.seq -o >/clusta/shah/local_progs/iprscan/test.out >SUBMITTED iprscan-20061114-12101842 > >FAILED > Iprscan job iprscan-20061114-12101842 failed and exit with status code 256 >/clusta/shah/local_progs/iprscan/bin/iprscan: >/clusta/shah/local_progs/iprscan/tmp/20061114/iprscan-20061114-12101842/iprscan-20061114-12101842.xml >unavailable : No such file or directory >/clusta/shah/local_progs/iprscan/bin/iprscan_wrapper.pl: failed to send error to >administrator: no destination address >Tool: iprscan >JobID: iprscan-20061114-12101842 >Time: Tue Nov 14 12:11:37 2006 >Error: > >supervise: doRawResults: failed to create XML output : > >Job submission parameters: >DD 14 >MM 11 >YYYY 2006 >appl hmmsmart,hmmpfam >cmd submit >crc 1 >format xml >frame 6 >hh 12 >jobid iprscan-20061114-12101842 >mm 10 >nseqs 3 >onego 1 >remotehost cccluster.uchicago.cc >seq.1.1.crc64 F94D07049A6D489D >seq.1.1.id RS16_ECOLI >seq.1.1.len 82 >seq.1.2.crc64 D44DAE8C544CB7C1 >seq.1.2.id Q9RHD9 >seq.1.2.len 267 >seq.1.3.crc64 CD84A335CCFFE6D7 >seq.1.3.id Y902_MYCTU >seq.1.3.len 446 >seqtype P >srchtype interactive >ss 18 >submission cli >tool iprscan > >NOTE: the newlines have been replaced with backslash. >---------------------------------------------------------- > > > > You should send this query direclty to interhelp at ebi.ac.uk, who can help. >Message: 4 >Date: Wed, 15 Nov 2006 12:41:13 +0000 (GMT) >From: Ulisses Dias >Subject: [BiO BB] Gene ontology PDB files >To: "General Forum at Bioinformatics.Org" > >Message-ID: <20061115124114.10256.qmail at web56613.mail.re3.yahoo.com> >Content-Type: text/plain; charset=iso-8859-1 > >Hi! > > Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term? > >Thank you > Ulisses Dias > > > The GOA database provides a file of PDB to GO annotations, see this page of downloades: http://www.ebi.ac.uk/GOA/downloads.html See the readme file for more info on the PDB GO annotations From Reactome-Knowledgebase at reactome.org Fri Nov 17 11:02:41 2006 From: Reactome-Knowledgebase at reactome.org (Reactome-Knowledgebase at reactome.org) Date: Fri, 17 Nov 2006 11:02:41 -0500 Subject: [BiO BB] Reactome 19 released Message-ID: The Reactome Knowledgebase team (Lincoln Stein's group at CSHL and Ewan Birney's group at European Bioinformatics Institute) is proud to announce the release of Reactome Version 19, accessible at http://www.reactome.org! Reactome is a curated knowledgebase of biological processes in humans. It covers 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, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). Two way links between HapMap and Reactome have been enabled from this release. Version 19 marks the completion of "Early phase of HIV life cycle" with the release of Uncoating, Reverse Transcription and Integration under HIV Life Cycle. Other new modules include HIV Vpu protein interactions with host and Transport of Influenza virus RNPs into host nucleus under host pathogen interactions, signaling cascades mediated by Toll-like receptors 5,7/8,9-11, and cell cycle events mediated by p27/p21 proteins. The standard display feature allows the user to choose the focus species annotations - curated (for human) and electronically inferred (for 22 other species). A feature for version tracking using stable identifiers has been enabled. Updated release statistics and the Editorial Calendar are available. 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 ulimard at yahoo.com.br Sat Nov 18 17:24:45 2006 From: ulimard at yahoo.com.br (Ulisses Dias) Date: Sat, 18 Nov 2006 22:24:45 +0000 (GMT) Subject: [BiO BB] Gene ontology PDB files In-Reply-To: <455C68EF.4000702@york.ac.uk> Message-ID: <754669.59195.qm@web56607.mail.re3.yahoo.com> Hi David Thank you so much for your reply. However I have a doubt using the browse and download csv tools. For example, I've clicked on Browse Database then Molecular Function and I get a tree of functions categories on the right that I can expand by clicking on the arrows. Following 'binding' then 'nucleic acid binding', I click on 'DNA binding (Go ID: 3677) and the first PDB ID that I get is the '10MH', but when I use the 'Custom Report' tool this structure id appears with the GO ID = 'n/a'. This kind of problem happens with some others structures. Please, tell me if I'm trying something wrong. Once again, thank you so much! Ulisses Dias DGW escreveu: Hi, You can search/browse the PDB by GO term from this URL http://www.rcsb.org/pdb/static.do?p=search/index.html. You may need to have popups enabled on your browser. For example, I can click on Browse Database then Molecular Function and I get a tree of function categories on the right that I can expand by clicking on the arrows. Following 'binding' then 'nucleic acid binding', I click on RNA binding (GO ID:3723) and get 537 structures. The PDB IDs can be pulled out by using the options under Tabulate. You may need to know the hierarchy of the GO terms you are interested, e.g. from AmiGO, as it doesn't appear to be easy to search directly for the term of interest at the PDB site. Also, you are not guaranteed to find everything of interest - I think the PDB only considers a subset of all the available GO terms and even then not all PDB entries have GO terms assigned to them. If you need to be more comprehensive you might have to BLAST all your gene products against the PDB. Hope this helps! David Ulisses Dias wrote: > Hi! > > Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term? > > Thank you > Ulisses Dias > > > > __________________________________________________ > 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 > _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Novidade no Yahoo! Mail: receba alertas de novas mensagens no seu celular. Registre seu aparelho agora! From dgw106 at york.ac.uk Sun Nov 19 05:58:35 2006 From: dgw106 at york.ac.uk (David G Waterman) Date: Sun, 19 Nov 2006 10:58:35 +0000 Subject: [BiO BB] Gene ontology PDB files In-Reply-To: <754669.59195.qm@web56607.mail.re3.yahoo.com> References: <754669.59195.qm@web56607.mail.re3.yahoo.com> Message-ID: <456038DB.30200@york.ac.uk> You're right. That's quite surprising (and not a little frustrating). I'm not sure of the reason for this. It might be time to contact the PDB helpdesk (info at rcsb.org), or perhaps try Pooja's link for GO assignments for PDB entries made by the GOA group at the EBI. Cheers D Ulisses Dias wrote: > Hi David > > Thank you so much for your reply. However I have a doubt using the browse and download csv tools. > > For example, I've clicked on Browse Database then Molecular Function and I get a tree of functions categories on the right that I can expand by clicking on the arrows. Following 'binding' then 'nucleic acid binding', I click on 'DNA binding (Go > ID: 3677) and the first PDB ID that I get is the '10MH', but when I use the 'Custom Report' tool this structure id appears with the GO ID = 'n/a'. This kind of problem happens with some others structures. > > Please, tell me if I'm trying something wrong. > > Once again, thank you so much! > > Ulisses Dias > > DGW escreveu: Hi, > > You can search/browse the PDB by GO term from this URL > http://www.rcsb.org/pdb/static.do?p=search/index.html. You may need to > have popups enabled on your browser. For example, I can click on Browse > Database then Molecular Function and I get a tree of function categories > on the right that I can expand by clicking on the arrows. Following > 'binding' then 'nucleic acid binding', I click on RNA binding (GO > ID:3723) and get 537 structures. The PDB IDs can be pulled out by using > the options under Tabulate. > > You may need to know the hierarchy of the GO terms you are interested, > e.g. from AmiGO, as it doesn't appear to be easy to search directly for > the term of interest at the PDB site. Also, you are not guaranteed to > find everything of interest - I think the PDB only considers a subset of > all the available GO terms and even then not all PDB entries have GO > terms assigned to them. If you need to be more comprehensive you might > have to BLAST all your gene products against the PDB. > > Hope this helps! > David > > Ulisses Dias wrote: > >> Hi! >> >> Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term? >> >> Thank you >> Ulisses Dias >> >> >> >> __________________________________________________ >> 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 >> >> > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > --------------------------------- > Novidade no Yahoo! Mail: receba alertas de novas mensagens no seu celular. Registre seu aparelho agora! > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From valenti at dsi.unimi.it Sun Nov 19 06:26:57 2006 From: valenti at dsi.unimi.it (Giorgio Valentini) Date: Sun, 19 Nov 2006 12:26:57 +0100 Subject: [BiO BB] CFP CIBB 2007 Message-ID: <45603F81.2020506@dsi.unimi.it> Dear colleague, We would like to invite you to participate in CIBB 2007, the Fourth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, that will be held in the wonderful location of Portofino Vetta (near Genova, Italy) from 7 to 10 July 2007. CIBB 2007 is jointly organized by - INNS, International Neural Network Society, SIG Bioinformatics - DSI, Dipartimento di Scienze dell'Informazione, Unversit? degli Studi di Milano. - DMI, Dipartimento di Matematica e Informatica, Universit? di Salerno and in connection with WILF 2007 (http://wilf2007.disi.unige.it). If you would like to contribute then please send a paper no more than 6 pages long in pdf format within 31th January 2007 to the meeting submission website http://cibb07.dsi.unimi.it/ and a copy in attachment to infocibb07 at dsi.unimi.it. We are looking forward to meet you in Portofino! Roberto Tagliaferri and Giorgio Valentini CIBB 2007 Meeting e-mail: infocibb07 at dsi.unimi.it Meeting website: http://cibb07.dsi.unimi.it ********************* Meeting description: ********************* The main goal of this meeting is to provide a forum open to researchers from different disciplines to present and discuss problems relative to computational techniques in bioinformatics with a particular focus on supervised and unsupervised machine learning methods. Topics of interest include, but are not limited to: sequence analysis; transcriptomics; proteomics; evolution and philogeny; comparative genomics; bio-medical text mining and imaging; heterogeneous data integration for diagnostics. For a more detailed list of covered research areas, please visit our website: http://cibb07.dsi.unimi.it. ********************* Paper submission: ********************* Papers must be written in Latex in LNCS Springer format following the guidelines for "Proceedings and Other Multi-author Volumes (http://www.springer.com). Papers must be no longer than 6 pages, including a cover sheet stating paper title, keyword(s), authors names and affiliations, contact author's name and contact details including telephone/fax numbers and e-mail address, and an abstract no more than 200 words long. CIBB 2007 is organized in connection with WILF 2007. For electronic submission and details about the format of the paper, please refer to the CIBB website (http://cibb07.dsi.unimi.it). All accepted papers submitted by registered participants to CIBB 2007 will be published in the Lecture Notes on Computer Science Series, Springer. Selected papers will be invited to submit an extended version for a special issues of an international journal. ********************* Important Dates: ********************* Submission deadline: January 31 2007 Notification of acceptance: February 28 2007 Final papers due: March 31 2007 Workshop: 7-10 July 2007. ********************* Organizers: ********************* Roberto Tagliaferri, Universit? di Salerno, Italy Giorgio Valentini, Universit? degli Studi di Milano, Italy ****************************************** Scientific Program Committee: ****************************************** Pierre Baldi, University of California, Irvine, USA Alberto Bertoni, Universit? degli Studi di Milano, Italy Paola Campadelli, Universit? degli Studi di Milano, Italy Nello Cristianini, University of Bristol, UK Giovanni Cuda, Universit? di Catanzaro, Italy Diego di Bernardo, Telethon Institute of Genetics and Medicine, Italy Joaquin Dopazo, Centro de Investigaci?n Pr?ncipe Felipe, Valencia, Spain Sandrine Dudoit, University of California, Berkeley, USA Jon Garibaldi, University of Nottingham, UK Emmanuel Ifeachor, University of Plymouth, UK Nathan Intrator, Tel Aviv University, Israel Nik Kasabov, Auckland University of Technology, NZ Natalio Krasnogor, University of Nottingham, UK Sushmita Mitra, Indian Statistical Institute, Kolkata, India Marco Muselli, CNR Genova, Italy Oleg Okun, University of Oulu, Finland Alberto Paccanaro,Yale University, CT, USA Giulio Pavesi, Universit? degli Studi di Milano, Italy David Alejandro Pelta, University of Granada, Spain Graziano Pesole, Universit? di Bari, Italy Leif E. Peterson, Baylor College of Medicine Houston, TX, USA Volker Roth, ETH Zurich, Switzerland Udo Seiffert, Leibniz Institute, Gatersleben, Germany Anna Tramontano, Universit? di Roma "La Sapienza", Italy Jean Philippe Vert, Centre for Computational Biology Ecole des Mines de Paris, France *************************************************************** -- =========================================== Giorgio Valentini D.S.I. - Universita' degli Studi di Milano - Italia Phone: +39 (02) 503.16225 e-mail: valentini at dsi.unimi.it http://homes.dsi.unimi.it/~valenti =========================================== From xiaowei.jiang at msn.com Mon Nov 20 06:23:19 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Mon, 20 Nov 2006 12:23:19 +0100 Subject: [BiO BB] Re: Ferguson plots In-Reply-To: <20061118170049.DBA8F36849E@primary.bioinformatics.org> Message-ID: Dear David, For analysing data from gel electrophoresis, please refer to the software "BioNumercis", where you might find something interesting. http://www.applied-maths.com/bionumerics/bionumerics.htm Please note that this is a comercial software. Kind regards, Xiaowei JIANG -----Original Message----- Today's Topics: 1. Ferguson plots (David G Waterman) ---------------------------------------------------------------------- Message: 1 Date: Sat, 18 Nov 2006 14:54:48 +0000 From: David G Waterman Subject: [BiO BB] Ferguson plots To: "General Forum at Bioinformatics.Org" Message-ID: <455F1EB8.5030803 at york.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi everyone, Does anyone know of a program for the PC that is capable of analysing gel electrophoresis data, in the form of relative mobilities, to generate a Ferguson plot? I found the Elphofit software via Google, but only managed to locate a Mac version, and I don't have access to a Mac at the moment. I've been using a spreadsheet to make the plot so far, but I think I could benefit from the analyses that a progam specific for the task may provide. Cheers, David ------------------------------ _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest, Vol 25, Issue 14 ************************************************** From aloraine at gmail.com Wed Nov 22 14:46:56 2006 From: aloraine at gmail.com (Ann Loraine) Date: Wed, 22 Nov 2006 13:46:56 -0600 Subject: [BiO BB] question regarding hit tracking software Message-ID: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> Greetings all! I'm looking for software that can track the number of accesses over time of specific files on a Web site (Apache). This is to collect usage statistics for a grant application, not to spy on users :-) Does anyone on the list have recommendations of good software I could use for this? Yours, Ann -- Ann Loraine Assistant Professor Departments of Genetics, Biostatistics, and Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org From ryan.raaum at gmail.com Thu Nov 23 09:32:27 2006 From: ryan.raaum at gmail.com (Ryan Raaum) Date: Thu, 23 Nov 2006 09:32:27 -0500 Subject: [BiO BB] question regarding hit tracking software In-Reply-To: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> References: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> Message-ID: On 11/22/06, Ann Loraine wrote: > > Greetings all! > > I'm looking for software that can track the number of accesses over > time of specific files on a Web site (Apache). > > This is to collect usage statistics for a grant application, not to > spy on users :-) > > Does anyone on the list have recommendations of good software I could > use for this? If it's a web page (rather than files that are being downloaded), Google Analytics is free and easy. I use it on all my sites. http://www.google.com/analytics Best, -Ryan Yours, > > Ann > > -- > Ann Loraine > Assistant Professor > Departments of Genetics, Biostatistics, and > Section on Statistical Genetics > University of Alabama at Birmingham > http://www.ssg.uab.edu > http://www.transvar.org > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Ryan Raaum http://raaum.org http://locomotive.raaum.org -- Self contained one-click Rails for Mac OS X From wilfred at sdsc.edu Wed Nov 22 15:24:49 2006 From: wilfred at sdsc.edu (Wilfred Li) Date: Wed, 22 Nov 2006 12:24:49 -0800 Subject: [BiO BB] question regarding hit tracking software In-Reply-To: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> Message-ID: <452F37AE49199D49B1702D7D45038C4D7F8306@et.ad.sdsc.edu> Google analytics is gaining popularity nowadays. Other software that we use includes analog http://www.analog.cx. Regards, Wilfred -----Original Message----- From: bio_bulletin_board-bounces+wilfred=sdsc.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+wilfred=sdsc.edu at bioinformatics.org] On Behalf Of Ann Loraine Sent: Wednesday, November 22, 2006 11:47 AM To: General Forum at Bioinformatics.Org Subject: [BiO BB] question regarding hit tracking software Greetings all! I'm looking for software that can track the number of accesses over time of specific files on a Web site (Apache). This is to collect usage statistics for a grant application, not to spy on users :-) Does anyone on the list have recommendations of good software I could use for this? Yours, Ann -- Ann Loraine Assistant Professor Departments of Genetics, Biostatistics, and Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From natarajanganesan at gmail.com Wed Nov 22 16:22:24 2006 From: natarajanganesan at gmail.com (Natarajan Ganesan) Date: Wed, 22 Nov 2006 16:22:24 -0500 Subject: [BiO BB] question regarding hit tracking software In-Reply-To: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> References: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> Message-ID: <91fe74380611221322x7b7bc549ra65feab29fe63f21@mail.gmail.com> Google analytics is one good tool. I have also found statcounter to be very useful (a free tool limited to last 100 users). I use both of these by putting their code on my web based sequence anaysis tools. I didnt know they could be used as a supporting statistic for grant aaplications. Thanks for the info Natarajan Ganesan, PhD nattu at gwu.edu On 11/22/06, Ann Loraine wrote: > > Greetings all! > > I'm looking for software that can track the number of accesses over > time of specific files on a Web site (Apache). > > This is to collect usage statistics for a grant application, not to > spy on users :-) > > Does anyone on the list have recommendations of good software I could > use for this? > > Yours, > > Ann > > -- > Ann Loraine > Assistant Professor > Departments of Genetics, Biostatistics, and > Section on Statistical Genetics > University of Alabama at Birmingham > http://www.ssg.uab.edu > http://www.transvar.org > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From ybolo001 at student.ucr.edu Wed Nov 22 17:49:21 2006 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Wed, 22 Nov 2006 14:49:21 -0800 Subject: [BiO BB] question regarding hit tracking software In-Reply-To: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> References: <83722dde0611221146s3d04f73bpcb25a064afa55ad8@mail.gmail.com> Message-ID: <941fcc750611221449k39cf9444maaadb10c7e87f8e8@mail.gmail.com> http://www.xav.com/scripts/axs/ This worked great for me. Apache keeps logs but if you are not root you cant get to them. Eugene On 11/22/06, Ann Loraine wrote: > > Greetings all! > > I'm looking for software that can track the number of accesses over > time of specific files on a Web site (Apache). > > This is to collect usage statistics for a grant application, not to > spy on users :-) > > Does anyone on the list have recommendations of good software I could > use for this? > > Yours, > > Ann > > -- > Ann Loraine > Assistant Professor > Departments of Genetics, Biostatistics, and > Section on Statistical Genetics > University of Alabama at Birmingham > http://www.ssg.uab.edu > http://www.transvar.org > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From roy at colibase.bham.ac.uk Thu Nov 23 13:33:15 2006 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 23 Nov 2006 18:33:15 +0000 Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 25, Issue 17 In-Reply-To: <20061123170102.C1F5C368CF2@primary.bioinformatics.org> References: <20061123170102.C1F5C368CF2@primary.bioinformatics.org> Message-ID: <4565E96B.4000502@colibase.bham.ac.uk> > I'm looking for software that can track the number of accesses over > time of specific files on a Web site (Apache). > > This is to collect usage statistics for a grant application, not to > spy on users :-) > > Does anyone on the list have recommendations of good software I could > use for this? AWStats is good for this- in fact you may find it gives you almost too many different statistics. It works by analysing log files so you can backdate your stats as far as your log record goes. http://awstats.sourceforge.net/ Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow Division of Immunity and Infection University of Birmingham, U.K. http://xbase.bham.ac.uk From jeff at bioinformatics.org Mon Nov 27 15:57:16 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 27 Nov 2006 15:57:16 -0500 Subject: [BiO BB] Course: Introduction to Bioinformatics Programming: Perl & R for Biologists I Message-ID: <456B512C.4030408@bioinformatics.org> (We apologize for multiple copies of this announcement. If you know some biologists who would like to learn the basics of bioinformatics programming, please give them this announcement. Bioinformatics.Org is non-profit, and the revenue from our courses helps to keep our free services on-line.) Bioinformatics.Org will be running an on-line version of the well-received, "Introduction to Bioinformatics Programming: Perl & R for Biologists I" (Open Source Bioinformatics for Researchers), which was originally held on-site. Note that this is not a static tutorial but live instruction using interactive "Webinar" software and voice conferencing that will closely replicate the on-site version of the course. LOCALE: On-line (instructions will be given) DATES: January 8-12, 2007 OVERVIEW: This is an on-line course on the fundamentals of open-source programming. It will help biologists understand how and when to use standard programming methods to solve computational biology problems, whether sequence analysis, gene expression, mass spectrometry, or systems biology. This course is modularized so that researchers can understand two distinct tools: a scripting language such as Perl, and a data analysis/visualization language such as R. Armed with some knowledge and hands-on experience with these tools, scientists will be able to perform basic software development tasks and be able to phrase research questions in the context of these tools. As a result, they will be able to appreciate and use computers better in their organization, and communicate better with their IT group. TOPICS: The first part of the course will cover the basics of Perl, including installing and running simple Perl scripts; variables (scalars, arrays); variable interpolation; printing; string operations; mathematical, conditional and logical operators; file input/output; loops (if-then-else, for, while); list operations; regular expressions; and functions. BioPerl will also be introduced. Afterward, students will be assigned a Perl project. The second part of the course will cover the basics of R, including installing and running R; understanding the R interactive environment; creating, storing and manipulating R data objects; reading data from files; applying built-in functions on data; for-loops; if-then-else statements; scripts; functions; and packages. Bioconductor will also be introduced. Afterward, students will be assigned an R project. SCHEDULE: The course will run during the week of January 8 with about 3 hours of instruction starting at 16:30 UTC each day. To find out more information on the course, including the registration process, please see the course schedule page: http://edu.bioinformatics.org/06b Also of note, this course introduces the "full-time student" tuition rate, which is just one-third of the commercial rate. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From xiaowei.jiang at msn.com Mon Nov 27 18:54:47 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Tue, 28 Nov 2006 00:54:47 +0100 Subject: [BiO BB] Issue about Spam In-Reply-To: <20061125170157.A46F1369679@primary.bioinformatics.org> Message-ID: Dear admin, I keep receiving spams. I also found my email adress exposed on the internet with conversations from this discuss group. you only simply replace user's email adress by "someone at domainname" e.g. mine "xiaowei.jiang at msn.com" , which is too simple. Please do sth to improve this situation. Kind regards, Xiaowei JIANG From idoerg at burnham.org Mon Nov 27 19:45:01 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon, 27 Nov 2006 16:45:01 -0800 Subject: [BiO BB] Issue about Spam In-Reply-To: References: Message-ID: <456B868D.7050409@burnham.org> Check the archives. The addresses are masked. Xiaowei JIANG wrote: > > Dear admin, > > I keep receiving spams. I also found my email adress exposed on the internet > with conversations from this discuss group. > > you only simply replace user's email adress by > "someone at domainname" e.g. mine "xiaowei.jiang at msn.com" , which is too > simple. > Please do sth to improve this situation. > > > Kind regards, > Xiaowei JIANG > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9949 http://iddo-friedberg.org http://BioFunctionPrediction.org From valenti at dsi.unimi.it Tue Nov 28 04:58:45 2006 From: valenti at dsi.unimi.it (Giorgio Valentini) Date: Tue, 28 Nov 2006 10:58:45 +0100 Subject: [BiO BB] AIIM special issue for CIBB 2007 Message-ID: <456C0855.6020500@dsi.unimi.it> Dear colleague, We are pleased to announce that the authors of the best papers accepted at CIBB 2007 will be invited to submit an extended version to a special issue of Artificial Intelligence in Medicine on "Computational Intelligence methods for Bioinformatics and Biostatistics". We recall that CIBB 2007, the Fourth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (http://cibb07.dsi.unimi.it) will be held in the wonderful location of Portofino Vetta (near Genova, Italy) from 7 to 10 July 2007. CIBB 2007 is jointly organized by - INNS, International Neural Network Society, SIG Bioinformatics - BITS, Bioinformatics ITalian Society - SIREN, Italian Society of Neural Networks - DSI, Dipartimento di Scienze dell'Informazione, Unversit? degli Studi di Milano. - DMI, Dipartimento di Matematica e Informatica, Universit? di Salerno and in connection with WILF 2007 (http://wilf2007.disi.unige.it). We are looking forward to meet you in Portofino! Roberto Tagliaferri and Giorgio Valentini CIBB 2007 Meeting e-mail: infocibb07 at dsi.unimi.it Meeting website: http://cibb07.dsi.unimi.it -- =========================================== Giorgio Valentini D.S.I. - Universita' degli Studi di Milano - Italia Phone: +39 (02) 503.16225 e-mail: valentini at dsi.unimi.it http://homes.dsi.unimi.it/~valenti =========================================== From kannaiah at bsd.uchicago.edu Tue Nov 28 12:10:30 2006 From: kannaiah at bsd.uchicago.edu (Annaiah, Kiran [BSD] - HGD) Date: Tue, 28 Nov 2006 11:10:30 -0600 Subject: [BiO BB] SNP question Message-ID: <1E383EBC90DB4E40B4312AA4ECD7542E3941DD@ADM-EXCHVS01.bsdad.uchicago.edu> Hello, I have a bunch of SNPS (rs) and want to extract sequences 150bp upstream and downstream of it. I have used dbSNP database and have got the sequence info in FASTA format, although the length of the sequence(upstream and downstream) they return varies. Anywhere else i could go to get this info? I am looking at BIOMART and UCSC table browser right now. Havent figured it out yet. Also when i get the 150bp sequence (up and downstream), i would like to know if any other SNP's exist in that region so i dont end up using that part of the sequence in my primer design process(end goal). Right now dbSNP does not tell me if there are any SNPs in the 150bp region around the SNP i submitted. Any suggestions would be helpful. thank you hak This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. From jeff at bioinformatics.org Tue Nov 28 17:12:25 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 28 Nov 2006 17:12:25 -0500 Subject: [BiO BB] Issue about Spam In-Reply-To: References: Message-ID: <456CB449.9060506@bioinformatics.org> (Yes, we know this is being posted to the whole list ;-) ) Spambots are a lot more sophisticated than they used to be. Even attempts to disguise addresses by using (usernospam at domainnospam dot comnospam) can be foiled by the use of RegEx matches. But, fret not, BiO is starting to incorporate CAPTCHAs and other ways to hide email addresses. Cheers, Jeff Xiaowei JIANG wrote: > > I keep receiving spams. I also found my email adress exposed on the > internet with conversations from this discuss group. you only simply > replace user's email adress by "someone at domainname" e.g. mine > "xiaowei.jiang at msn.com" , which is too simple. Please do sth to > improve this situation. -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From xiaowei.jiang at msn.com Wed Nov 29 13:31:38 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Wed, 29 Nov 2006 19:31:38 +0100 Subject: [BiO BB] Re: Issue about Spam In-Reply-To: <20061129170221.B943F36864A@primary.bioinformatics.org> Message-ID: Dear Jeff and other fellows, I thank you for your reply. I am sorry to put this topic here (not necessarily related to Bioinformatics). I kindly inform everyone in this group that you should carefully choose your email address for the discussion purpose in this group. Because there is a probability (recently I have got 5 spams, so you should have the same chance to get spams as I do) that your email address can be collected by Spambots from Internet. So you should keep that in mind before this issue is smartly solved since the Spambots nowadays are getting smart. :) P.S. The spam is a kind of fraud email related to research funding stuff. Kind regards, Xiaowei JIANG From gilbertd at oat.bio.indiana.edu Tue Nov 28 21:25:27 2006 From: gilbertd at oat.bio.indiana.edu (Don Gilbert) Date: Tue, 28 Nov 2006 21:25:27 -0500 (EST) Subject: [BiO BB] GenBank 1996 CD-ROM releases sought for historical archive Message-ID: <200611290225.kAT2PRW26265@net.bio.net> Dear folks, There is a historical archive of GenBank releases from when it was distributed on CD-ROM, drawn from my old disk collection. I would like to fill in missing releases from 1996, just before NCBI ceased producing these. Find this archive at ftp://bio-mirror.net/biomirror-archive/ If you have a copy of NCBI-GenBank (Flat File Format) or Entrez:Sequences multi-CD-ROM produced after April 1996 (rel94), please contact me. This would include GenBank release numbers 95,96,97,98. Release 98 may have been the last CD-ROM release. Also if you have archival copies of the post-CD releases from 1997 to 2004 you would like to contribute to this archive, please let me know. Most people don't care about these historical releases, as the data, possibly updated and corrected, is available in current releases. For some critical purposes, research using the older data requires these historical data releases be available for confirmation. Thanks, Don Gilbert gilbertd at net.bio.net From gigi at biocomp.unibo.it Wed Nov 29 07:11:18 2006 From: gigi at biocomp.unibo.it (gigi) Date: Wed, 29 Nov 2006 13:11:18 +0100 Subject: [BiO BB] BOLOGNA WINTER SCHOOL 2007: Bioinformatics for S&S Biology In-Reply-To: <456C0855.6020500@dsi.unimi.it> References: <456C0855.6020500@dsi.unimi.it> Message-ID: <456D78E6.401@biocomp.unibo.it> Dear collegue, we are pleased to announce the: Bologna Winter School 2007 BIOINFORMATICS FOR SYSTEMS AND SYNTHETIC BIOLOGY New approaches and algorithms to cope with the future of Biological Science Bologna (Italy) February 18-23, 2007 http://www.biocomp.unibo.it/~school2007/ APPLICATION should be submitted to: school2007 @ biocomp . unibo . it Biologists for decades have adopted a reductionist approach to investigate the secret of life. In recent years however, thanks to the genome sequencing efforts, new/old disciplines gained prominence with the specific aim of studying at a global scale biological processes in terms of their molecular constituents and their functional interactions. This is the case of Systems Biology, not new in terms of name and definition that presently takes advantage of new technological developments to investigate biological processes at cell, organism or communicative level. Based on high-throughput quantitative measurements, Systems Biology adopts computational modelling, mathematical, control and optimization theories with the purpose of reconstructing cellular systems and their functioning. Even more recently, Synthetic Biology seeks to engineer complex artificial biological systems starting from molecular components to investigate natural biological phenomena for a variety of applications to come. Can Bioinformatics gap the bridge from molecular to multi-level and integrated modelling and be the link among Systems and Synthetic Biology? The Bologna School will focus on the present state of art of Bioinformatics, from data analysis to their integration and assessment in relation to problems of Systems and Synthetic Biology. The main topics that will be explained and debated are: ? Bionformatics in relation to System and Synthetic Biology ? Genomic networks and their modelling: the state of the art ? Progress in protein structure prediction and protein engineering ? Computational methods for Systems and Synthetic Biology ? Role of Synthetic Biology in the development of new powerful advanced technologies The school will cover different sessions: The frontiers of Structural and Functional Genomics Data integration, knowledge mining and visualization of systems biology data High throughput experiments and Data Bases Modelling the data: towards a reconstruction of biological systems. Synthetic Biology: putting engineering into biology Each day four lectures and/or demos will be given to the students. An open forum for discussion on hot topics will be held during the round table discussion: " Bionanotechnologies and Nanobiotechnologies for Systems and Synthetic Biology ". Students may sign up for short oral presentations during the student's corner. TEACHERS: Patrick Aloy Institute for Research in Biomedicine, Barcelona, ES Luca Benini University of Bologna, IT Alvis Brazma European Bioinformatics Institute, Hinxton, UK S?ren Brunak Technical University of Denmark, Lyngby, DK Rita Casadio University of Bologna, IT Silvio Cavalcanti University of Bologna, IT Giovanni De Micheli Ecole Polytechnique F?d?rale, Lausanne, CH Diego Di Bernardo Telethon Institute of Genetics and Medicine, Napoli, IT Joaquin Dopazo Centro de Investigaci?n "Principe Felipe", Valencia, ES Roderic Guig? University "Pompeu Fabra" Barcelona, ES David T. Jones University College, London, UK Arthur Lesk PennState University, University Park, USA Michal Linial The Hebrew University, Jerusalem, IL Marc Marti-Renom Centro de Investigaci?n "Principe Felipe", Valencia, ES Sven Panke Swiss Federal Institute of Technology, Z?rich, CH Juan Poyatos Centro Nacional de Investigaciones Oncol?gicas, Madrid, ES Reinhard Schneider European Molecular Biology Laboratory, Heidelberg, DE Luis Serrano European Molecular Biology Laboratory, Heidelberg, DE Anna Tramontano University "La Sapienza", Roma, IT Alfonso Valencia Centro Nacional de Investigaciones Oncol?gicas, Madrid, ES PROGRAM MONDAY 19 The frontiers of Structural and Functional Genomics/ TUESDAY 20 Data integration, knowledge mining and visualization of systems biology data WEDNESDAY 21 High throughput experiments and Data Bases Student's corner THURSDAY 22 Modelling the data: towards a reconstruction of biological systems Round Table Discussion: Bionanotechnologies and Nanobiotechnologies for Systems and Synthetic Biology FRIDAY 23 Synthetic Biology: putting engineering into biology organised by University of Bologna Faculty of Mathematical, Physical and Natural Sciences Faculty of Medicine CIRB INTERDEPARTMENTAL CENTER FOR BIOTECHNOLOGY CIG INTERDEPARTMENTAL CENTER "Luigi Galvani" FOR BIOINFORMATICS, BIOPHYSICS and BIOCOMPLEXITY DEIS DEPARTMENT OF ELECTRONICS,COMPUTER SCIENCE AND SYSTEMS BioSapiens Network of Excellence (EU project, VI FP) BioDec Srl National Institute for Biostructures and Biosystems (INBB) FIRB for Bioinformatics (MIUR) Organisation: AIRBBC Associazione Italiana per la Ricerca in Biofisica e Biologia Computazionale