From hlapp at drycafe.net Mon Aug 1 18:36:27 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 1 Aug 2011 18:36:27 -0400 Subject: [Open-bio-l] Job opportunity: User Interface Design and Web Application Developer Message-ID: <7F0AE58E-6052-469B-ACD0-207FAD060472@drycafe.net> (Apologies if you have received this already or if this is considered spam - we're trying to reach out as broad as possible and I know that quite a few in the Bio* communities would be well qualified. Please feel free to pass on to anyone who might be interested, or might know someone who is.) User Interface Design and Web Application Developer The National Evolutionary Synthesis Center (NESCent) seeks a creative and enthusiastic individual to design user interfaces and web applications for scientific applications that manage, analyze, visualize and share data in support of evolutionary research. The incumbent will work as part of a small informatics team in close collaboration with domain scientists. NESCent (http://nescent.org) is an NSF-funded center dedicated to cross-disciplinary research in evolutionary science. Our informatics team works closely with visiting and resident scientists to support their custom software and database development needs (http://informatics.nescent.org ), and collaborates broadly with other biodiversity informatics projects. All NESCent software products are open-source, and the Center has a number of initiatives to actively promote collaborative development of community software resources. Above all, we are enthusiastic about our work, about the mission of the Center, and about the contribution of informatics to that mission. Job description: The incumbent will design and develop user interfaces and web applications for databases and other software tools for sponsored scientists and staff. The job responsibilities include all stages of the software development process, including requirements gathering, design, implementation, release packaging and documentation, as part of a small team (typically 2-3 individuals). We expect the incumbent to present their work at conferences and contribute to publications with scientific collaborators; interact regularly with visiting and resident scientists, other members of the informatics team and Center staff; and generally serve as an expert resource for Center personnel. The position provides opportunities for professional development and encourages research into new technologies. Most informatics staff work at our Durham NC offices, located adjacent to Duke University, but we support a wide range of technologies for virtual communication with off-site staff and collaborators. Salary range: $70,000 - $80,000, depending on education and experience Required Qualifications: * Demonstrated success collaborating with clients on custom software solutions * Experience with various stages of the software development cycle * Expertise in development and testing of user interface designs * Excellent communication skills, both virtual and face-to-face Preferred Qualifications: * M.S. or Ph.D. in Computer Science, Bioinformatics or related field * Demonstrated interest in science, particularly biology * Expertise in dynamic and interactive web technologies (JavaScript, CGI) * Expertise in rapid application development and respective programming technologies and languages (e.g., modern scripting languages and web-application frameworks such as Python/Django, Ruby/ Ruby-on-Rails, and Perl/Catalyst). * Expertise in graphic design * Expertise in data visualization and/or scientific data integration * Expertise in software usability design and assessment * Expertise in web service (SOAP, REST, XML, JSON) and semantic web technologies * Fluency in Java programming * Prior experience in relational database programming (PostgreSQL or MySQL) * Experience with open-source, and collaborative, software development How to apply: Please send cover letter, resume and contact information for three references to Dr. Karen Cranston, Training Coordinator and Bioinformatics Project Manager (karen.cranston at nescent.org); Please also complete the online application at the University of North Carolina HR website: http://bit.ly/r9HQ8r. Informal inquires or requests for additional information may be directed to Dr. Cranston by email or phone (+1-919-613-2275). Closing date is August 15, 2011. -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Tue Aug 9 16:09:05 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 9 Aug 2011 15:09:05 -0500 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: I'm reviving this thread to see what the current status is (if anything has changed). The bioperl parser has the same problem; at the moment we're bascially stuck until NCBI gives some indication as to whether this is a bug or not. Any word back from them yet? (and agreed, it would be nice to have an external bug tracker from NCBI). chris On May 4, 2011, at 5:36 AM, Peter Cock wrote: > On Wed, May 4, 2011 at 10:59 AM, Michal wrote: >> Hi Peter, >> Do you have the script which read >> >> https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml >> >> >> and what would be the correct output? >> >> Thank you in advance. >> >> Cheers, >> Michal > > Hi Michal, > > I'm not quite sure what you're asking, but I'll try. First, the three > data files: > > $ wget https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml > $ wget https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/four_human_proteins.fasta > $ wget https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/rhodopsin_proteins.fasta > > The query file has four sequences, > > $ grep -c "^>" four_human_proteins.fasta > 4 > > $ grep "^>" four_human_proteins.fasta >> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 >> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 >> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 >> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 > > Based on past experience, I would expect 4 iteration blocks in the > XML, but in this case I have 24: > > $ grep "" -c blastp_four_human_vs_rhodopsin.xml > 24 > > Notice we get 6 iterations for each query (4 times 6 is 24): > > $ grep "" blastp_four_human_vs_rhodopsin.xml > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > > Now, using the two FASTA files directly and re-running blastp, what do I get? > > $ ~/Downloads/ncbi-blast-2.2.25+/bin/blastp -query > four_human_proteins.fasta -subject rhodopsin_proteins.fasta -outfmt 5 > | grep "" -c > 24 > > Or again with -parse_deflines, which changes how the hit ID/def is presented: > > $ ~/Downloads/ncbi-blast-2.2.25+/bin/blastp -query > four_human_proteins.fasta -subject rhodopsin_proteins.fasta -outfmt 5 > -parse_deflines | grep "" -c > 24 > > How about older versions? > > $ ~/Downloads/ncbi-blast-2.2.24+/bin/blastp -query > four_human_proteins.fasta -subject rhodopsin_proteins.fasta -outfmt 5 > BLAST engine error: XML formatting is only supported for a database search > > I'll have to make a blast database first... > > $ ~/Downloads/ncbi-blast-2.2.24+/bin/makeblastdb -in > rhodopsin_proteins.fasta -dbtype prot > > Building a new DB, current time: 05/04/2011 11:22:57 > New DB name: rhodopsin_proteins.fasta > New DB title: rhodopsin_proteins.fasta > Sequence type: Protein > Keep Linkouts: T > Keep MBits: T > Maximum file size: 1073741824B > Adding sequences from FASTA; added 6 sequences in 0.105655 seconds. > > $ ~/Downloads/ncbi-blast-2.2.25+/bin/blastp -query > four_human_proteins.fasta -db rhodopsin_proteins.fasta -outfmt 5 | > grep "" -c > 4 > > Look - just four identifiers as I expect! This also works if the database > is built with the -parse_seqids switch. > > The same happens with older versions of BLAST+, one > block per query, so four iteration blocks for this example. I tried all > of 2.2.21+, 2.2.22+, 2.2.23+ and 2.2.24+ (running makeblastdb to > give a fresh database, then blastp). > > That seems to demonstrate that bug is specific to the XML output > from FASTA vs FASTA (not FASTA vs DB), which is a new feature > in NCBI BLAST 2.2.25+ > > I will raise this with the NCBI, and report back. > > However, even if the NCBI fix it in the next release, we (Bio*) may > want to update our parsers to cope with this quirk, or at least put a > warning in our BLAST XML parser documentation, as there will be > lots of installations of NCBI BLAST 2.2.25+ in the wild. > > Peter From p.j.a.cock at googlemail.com Wed Aug 10 05:15:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 10 Aug 2011 10:15:18 +0100 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Tue, Aug 9, 2011 at 9:09 PM, Chris Fields wrote: > I'm reviving this thread to see what the current status is (if anything has > changed). ?The bioperl parser has the same problem; at the moment we're > bascially stuck until NCBI gives some indication as to whether this is a > bug or not. ?Any word back from them yet? > > (and agreed, it would be nice to have an external bug tracker from NCBI). > > chris Hi Chris, My email to the NCBI on 17 May had a reply from Tao Tao (NCBI User services) saying it would be brought to their developers' attention. For reference, the email subject line was: "Multiple iteration blocks per query in FASTA vs FASTA BLAST XML" I have just emailed back to enquire if there is any news to report. Peter From cjfields at illinois.edu Wed Aug 10 21:35:37 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Aug 2011 20:35:37 -0500 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Aug 10, 2011, at 4:15 AM, Peter Cock wrote: > On Tue, Aug 9, 2011 at 9:09 PM, Chris Fields wrote: >> I'm reviving this thread to see what the current status is (if anything has >> changed). The bioperl parser has the same problem; at the moment we're >> bascially stuck until NCBI gives some indication as to whether this is a >> bug or not. Any word back from them yet? >> >> (and agreed, it would be nice to have an external bug tracker from NCBI). >> >> chris > > Hi Chris, > > My email to the NCBI on 17 May had a reply from Tao Tao (NCBI User > services) saying it would be brought to their developers' attention. > > For reference, the email subject line was: > "Multiple iteration blocks per query in FASTA vs FASTA BLAST XML" > > I have just emailed back to enquire if there is any news to report. > > Peter Wonder if it's worth a second prod from someone else. Sometimes that gets their attention. chris From p.j.a.cock at googlemail.com Thu Aug 11 05:09:13 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 11 Aug 2011 10:09:13 +0100 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Thu, Aug 11, 2011 at 2:35 AM, Chris Fields wrote: >> Hi Chris, >> >> My email to the NCBI on 17 May had a reply from Tao Tao (NCBI User >> services) saying it would be brought to their developers' attention. >> >> For reference, the email subject line was: >> "Multiple iteration blocks per query in FASTA vs FASTA BLAST XML" >> >> I have just emailed back to enquire if there is any news to report. >> >> Peter > > Wonder if it's worth a second prod from someone else. ?Sometimes > that gets their attention. > > chris Tao replied yesterday morning (US time) to confirm the test files so he (she?) could try this on the latest code. Peter From p.j.a.cock at googlemail.com Fri Aug 12 04:53:48 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 12 Aug 2011 09:53:48 +0100 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Thu, Aug 11, 2011 at 2:35 AM, Chris Fields wrote: > > Wonder if it's worth a second prod from someone else. >?Sometimes that gets their attention. > > chris I've written a blog post on BLAST bug reporting (thanks for reading it Chris for a final sanity check / proof reading before I mentioned it on Twitter): http://blastedbio.blogspot.com/2011/08/opening-up-ncbi-blast.html So far no further follow up on the XML iteration issue from Tao at the NCBI since resending him the sample data files earlier this week. Peter From hlapp at drycafe.net Mon Aug 1 22:36:27 2011 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 1 Aug 2011 18:36:27 -0400 Subject: [Open-bio-l] Job opportunity: User Interface Design and Web Application Developer Message-ID: <7F0AE58E-6052-469B-ACD0-207FAD060472@drycafe.net> (Apologies if you have received this already or if this is considered spam - we're trying to reach out as broad as possible and I know that quite a few in the Bio* communities would be well qualified. Please feel free to pass on to anyone who might be interested, or might know someone who is.) User Interface Design and Web Application Developer The National Evolutionary Synthesis Center (NESCent) seeks a creative and enthusiastic individual to design user interfaces and web applications for scientific applications that manage, analyze, visualize and share data in support of evolutionary research. The incumbent will work as part of a small informatics team in close collaboration with domain scientists. NESCent (http://nescent.org) is an NSF-funded center dedicated to cross-disciplinary research in evolutionary science. Our informatics team works closely with visiting and resident scientists to support their custom software and database development needs (http://informatics.nescent.org ), and collaborates broadly with other biodiversity informatics projects. All NESCent software products are open-source, and the Center has a number of initiatives to actively promote collaborative development of community software resources. Above all, we are enthusiastic about our work, about the mission of the Center, and about the contribution of informatics to that mission. Job description: The incumbent will design and develop user interfaces and web applications for databases and other software tools for sponsored scientists and staff. The job responsibilities include all stages of the software development process, including requirements gathering, design, implementation, release packaging and documentation, as part of a small team (typically 2-3 individuals). We expect the incumbent to present their work at conferences and contribute to publications with scientific collaborators; interact regularly with visiting and resident scientists, other members of the informatics team and Center staff; and generally serve as an expert resource for Center personnel. The position provides opportunities for professional development and encourages research into new technologies. Most informatics staff work at our Durham NC offices, located adjacent to Duke University, but we support a wide range of technologies for virtual communication with off-site staff and collaborators. Salary range: $70,000 - $80,000, depending on education and experience Required Qualifications: * Demonstrated success collaborating with clients on custom software solutions * Experience with various stages of the software development cycle * Expertise in development and testing of user interface designs * Excellent communication skills, both virtual and face-to-face Preferred Qualifications: * M.S. or Ph.D. in Computer Science, Bioinformatics or related field * Demonstrated interest in science, particularly biology * Expertise in dynamic and interactive web technologies (JavaScript, CGI) * Expertise in rapid application development and respective programming technologies and languages (e.g., modern scripting languages and web-application frameworks such as Python/Django, Ruby/ Ruby-on-Rails, and Perl/Catalyst). * Expertise in graphic design * Expertise in data visualization and/or scientific data integration * Expertise in software usability design and assessment * Expertise in web service (SOAP, REST, XML, JSON) and semantic web technologies * Fluency in Java programming * Prior experience in relational database programming (PostgreSQL or MySQL) * Experience with open-source, and collaborative, software development How to apply: Please send cover letter, resume and contact information for three references to Dr. Karen Cranston, Training Coordinator and Bioinformatics Project Manager (karen.cranston at nescent.org); Please also complete the online application at the University of North Carolina HR website: http://bit.ly/r9HQ8r. Informal inquires or requests for additional information may be directed to Dr. Cranston by email or phone (+1-919-613-2275). Closing date is August 15, 2011. -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From cjfields at illinois.edu Tue Aug 9 20:09:05 2011 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 9 Aug 2011 15:09:05 -0500 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: I'm reviving this thread to see what the current status is (if anything has changed). The bioperl parser has the same problem; at the moment we're bascially stuck until NCBI gives some indication as to whether this is a bug or not. Any word back from them yet? (and agreed, it would be nice to have an external bug tracker from NCBI). chris On May 4, 2011, at 5:36 AM, Peter Cock wrote: > On Wed, May 4, 2011 at 10:59 AM, Michal wrote: >> Hi Peter, >> Do you have the script which read >> >> https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml >> >> >> and what would be the correct output? >> >> Thank you in advance. >> >> Cheers, >> Michal > > Hi Michal, > > I'm not quite sure what you're asking, but I'll try. First, the three > data files: > > $ wget https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml > $ wget https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/four_human_proteins.fasta > $ wget https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/rhodopsin_proteins.fasta > > The query file has four sequences, > > $ grep -c "^>" four_human_proteins.fasta > 4 > > $ grep "^>" four_human_proteins.fasta >> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 >> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 >> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 >> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 > > Based on past experience, I would expect 4 iteration blocks in the > XML, but in this case I have 24: > > $ grep "" -c blastp_four_human_vs_rhodopsin.xml > 24 > > Notice we get 6 iterations for each query (4 times 6 is 24): > > $ grep "" blastp_four_human_vs_rhodopsin.xml > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9BS26|ERP44_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|Q9NSY1|BMP2K_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P06213|INSR_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > sp|P08100|OPSD_HUMAN > > Now, using the two FASTA files directly and re-running blastp, what do I get? > > $ ~/Downloads/ncbi-blast-2.2.25+/bin/blastp -query > four_human_proteins.fasta -subject rhodopsin_proteins.fasta -outfmt 5 > | grep "" -c > 24 > > Or again with -parse_deflines, which changes how the hit ID/def is presented: > > $ ~/Downloads/ncbi-blast-2.2.25+/bin/blastp -query > four_human_proteins.fasta -subject rhodopsin_proteins.fasta -outfmt 5 > -parse_deflines | grep "" -c > 24 > > How about older versions? > > $ ~/Downloads/ncbi-blast-2.2.24+/bin/blastp -query > four_human_proteins.fasta -subject rhodopsin_proteins.fasta -outfmt 5 > BLAST engine error: XML formatting is only supported for a database search > > I'll have to make a blast database first... > > $ ~/Downloads/ncbi-blast-2.2.24+/bin/makeblastdb -in > rhodopsin_proteins.fasta -dbtype prot > > Building a new DB, current time: 05/04/2011 11:22:57 > New DB name: rhodopsin_proteins.fasta > New DB title: rhodopsin_proteins.fasta > Sequence type: Protein > Keep Linkouts: T > Keep MBits: T > Maximum file size: 1073741824B > Adding sequences from FASTA; added 6 sequences in 0.105655 seconds. > > $ ~/Downloads/ncbi-blast-2.2.25+/bin/blastp -query > four_human_proteins.fasta -db rhodopsin_proteins.fasta -outfmt 5 | > grep "" -c > 4 > > Look - just four identifiers as I expect! This also works if the database > is built with the -parse_seqids switch. > > The same happens with older versions of BLAST+, one > block per query, so four iteration blocks for this example. I tried all > of 2.2.21+, 2.2.22+, 2.2.23+ and 2.2.24+ (running makeblastdb to > give a fresh database, then blastp). > > That seems to demonstrate that bug is specific to the XML output > from FASTA vs FASTA (not FASTA vs DB), which is a new feature > in NCBI BLAST 2.2.25+ > > I will raise this with the NCBI, and report back. > > However, even if the NCBI fix it in the next release, we (Bio*) may > want to update our parsers to cope with this quirk, or at least put a > warning in our BLAST XML parser documentation, as there will be > lots of installations of NCBI BLAST 2.2.25+ in the wild. > > Peter From p.j.a.cock at googlemail.com Wed Aug 10 09:15:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 10 Aug 2011 10:15:18 +0100 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Tue, Aug 9, 2011 at 9:09 PM, Chris Fields wrote: > I'm reviving this thread to see what the current status is (if anything has > changed). ?The bioperl parser has the same problem; at the moment we're > bascially stuck until NCBI gives some indication as to whether this is a > bug or not. ?Any word back from them yet? > > (and agreed, it would be nice to have an external bug tracker from NCBI). > > chris Hi Chris, My email to the NCBI on 17 May had a reply from Tao Tao (NCBI User services) saying it would be brought to their developers' attention. For reference, the email subject line was: "Multiple iteration blocks per query in FASTA vs FASTA BLAST XML" I have just emailed back to enquire if there is any news to report. Peter From cjfields at illinois.edu Thu Aug 11 01:35:37 2011 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Aug 2011 20:35:37 -0500 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Aug 10, 2011, at 4:15 AM, Peter Cock wrote: > On Tue, Aug 9, 2011 at 9:09 PM, Chris Fields wrote: >> I'm reviving this thread to see what the current status is (if anything has >> changed). The bioperl parser has the same problem; at the moment we're >> bascially stuck until NCBI gives some indication as to whether this is a >> bug or not. Any word back from them yet? >> >> (and agreed, it would be nice to have an external bug tracker from NCBI). >> >> chris > > Hi Chris, > > My email to the NCBI on 17 May had a reply from Tao Tao (NCBI User > services) saying it would be brought to their developers' attention. > > For reference, the email subject line was: > "Multiple iteration blocks per query in FASTA vs FASTA BLAST XML" > > I have just emailed back to enquire if there is any news to report. > > Peter Wonder if it's worth a second prod from someone else. Sometimes that gets their attention. chris From p.j.a.cock at googlemail.com Thu Aug 11 09:09:13 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 11 Aug 2011 10:09:13 +0100 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Thu, Aug 11, 2011 at 2:35 AM, Chris Fields wrote: >> Hi Chris, >> >> My email to the NCBI on 17 May had a reply from Tao Tao (NCBI User >> services) saying it would be brought to their developers' attention. >> >> For reference, the email subject line was: >> "Multiple iteration blocks per query in FASTA vs FASTA BLAST XML" >> >> I have just emailed back to enquire if there is any news to report. >> >> Peter > > Wonder if it's worth a second prod from someone else. ?Sometimes > that gets their attention. > > chris Tao replied yesterday morning (US time) to confirm the test files so he (she?) could try this on the latest code. Peter From p.j.a.cock at googlemail.com Fri Aug 12 08:53:48 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 12 Aug 2011 09:53:48 +0100 Subject: [Open-bio-l] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour In-Reply-To: References: <398303E2-1195-4CC2-8B73-09C6C1117892@illinois.edu> <4DC12371.3040204@gmail.com> Message-ID: On Thu, Aug 11, 2011 at 2:35 AM, Chris Fields wrote: > > Wonder if it's worth a second prod from someone else. >?Sometimes that gets their attention. > > chris I've written a blog post on BLAST bug reporting (thanks for reading it Chris for a final sanity check / proof reading before I mentioned it on Twitter): http://blastedbio.blogspot.com/2011/08/opening-up-ncbi-blast.html So far no further follow up on the XML iteration issue from Tao at the NCBI since resending him the sample data files earlier this week. Peter