From quwubin at gmail.com Mon Sep 8 09:59:57 2008 From: quwubin at gmail.com (Wubin Qu) Date: Mon, 8 Sep 2008 21:59:57 +0800 Subject: [Biopython-announce] BioPythonGUI: Graphical User Interface for BioPython Message-ID: Hi all, I started a new project named BioPythonGUI for a few of days. The following is the 'About' page from BioPythonGUI project. BioPythonGUI is a Graphical User Interface of BioPython. BioPython is a widely used python module set in bioinformatics. It help researchers: - Parsing files in di fferent database formats - Interfaces into programs like Blast, Entrez and PubMed - A sequence class (can transcribe, translate, invert, etc) - Code for handling alignments of sequences - Clustering algorithms - etc. However, it's not everyone can use the BioPython, especially ones who do not know much about the programming. How can you expect a professor who never known about any programming to use BioPython to parse the BLAST report file? This is the problem which the BioPythonGUI would solve. I started the project with the goal "Everyone can use BioPython with BioPythonGUI". Until now, there are two modules SeqGUI and BlastGUI are available in BioPythonGUI. I would greatly appreciate if you use BioPythonGUI and send me the feedback. Please see the developer's blog for details. Project Blog: http://biopythongui.blogspot.com/ Download: https://sites.google.com/site/biopythongui/download Screenshots: http://picasaweb.google.com/quwubin/BioPythonGUI02# ______________________________ Best regards, Wubin Qu From mjldehoon at yahoo.com Wed Sep 10 10:14:49 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 10 Sep 2008 07:14:49 -0700 (PDT) Subject: [Biopython-announce] Biopython 1.48 released Message-ID: <701345.92946.qm@web62402.mail.re1.yahoo.com> We are pleased to announce the release of Biopython 1.48. Some new functionality has been added, a few bugs have been fixed, the documentation has been updated, plus several obsolete modules have been deprecated (or explicitly labelled as obsolete). The following additional file formats are now supported in Bio.SeqIO and Bio.AlignIO: * reading and writing "tab" format (simple tab separated) * writing "nexus" files * reading "pir" files (NBRF/PIR) * basic support for writing "genbank" files (GenBank plain text) This release also fixes some problems reading Clustal alignments (introduced in Biopython 1.46 when consolidating Bio.AlignIO and Bio.Clustalw), and some updates to the Bio.Sequencing parsers. The SeqRecord and Alignment objects have a new method to get the object as a string in a given file format (handled via Bio.SeqIO and Bio.AlignIO). Bio.PubMed and the online code in Bio.GenBank are now considered obsolete, and we intend to deprecate them after the next release. For accessing PubMed and GenBank, please use Bio.Entrez instead. Martel and Bio.Mindy are now considered to be obsolete, and are likely to be deprecated and removed in a future release, at which point we will drop the optional dependency on mxTextTools. Bio.Fasta is also considered to be obsolete, please use Bio.SeqIO instead. We do intend to deprecate this module eventually, however, for several years this was the primary FASTA parsing module in Biopython and is likely to be in use in many existing scripts. In addition a number of other modules have been deprecated, including: Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics - see the DEPRECATED file for full details. Source distributions are available from the Biopython website at http://biopython.org, and Windows installers will be added shortly. My thanks to all bug reporters, code contributors and others who made this new release possible. Peter, on behalf of the Biopython developers P.S. This message will be forwarded to the Biopython anoucement mailing list shortly. For those of you who prefer news readers to email lists, have a look at the OBF news server: http://news.open-bio.org/news/2008/09/biopython-release-148/ where there are Biopython news feeds available: http://news.open-bio.org/news/category/obf-projects/biopython/feed/rdf http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss2 http://news.open-bio.org/news/category/obf-projects/biopython/feed/atom From paolo.romano at istge.it Tue Sep 16 10:12:12 2008 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 16 Sep 2008 14:12:12 -0000 Subject: [Biopython-announce] CFP: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) Message-ID: <200809161414.m8GEEBou051606@ibm43p.biotech.ist.unige.it> Apologies, if you're receiving multiple copies. ---------------------------------------------------------------- International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 28th November 2008, Edinburgh, UK http://www.swat4ls.org/ CALL FOR PAPERS Overview -------- The workshop is organized in sessions and open discussions. Invited speakers will present state-of-the-art, provocative lectures on the workshop's main topic, while a number of submissions will be accepted as oral presentations and posters on all workshop's topics. Workshop Description -------------------- Semantic Web technologies, tools and applications are starting to emerge in Life Sciences. In recent years, systems have been introduced and an increasing interest among researchers is arising. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences. Keynote Speakers ------------------------ + Semantic web technology in translational cancer research, Michael Krauthammer, Department of Pathology, Yale University School of Medicine, USA + Using Ontologies to bring Web Services on to the Semantic Web Mark Wilkinson, Dept. of Medical Genetics, University of British Columbia, Canada Workshop Venue and Format ------------------------ The workshop will take place in Edinburgh, Scotland, on 28 November 2008, and is hosted by the e-Science Institute of the UK's National e-Science Centre (NeSC). SWAT4LS will be a one-day workshop and will consist of two invited talks, regular paper and poster presentations. The workshop will conclude with a panel discussion on the strength and weaknesses of the Semantic Web for the Life Sciences. Deadlines --------- * Submission deadline (both papers and posters): 30 September 2008 * Notification of acceptance: 20 October 2008 * Camera-ready submission: 3 November 2008 (Authors who are interested in submitting a paper/poster to the workshop, but may require a short extension to the deadline, should get in touch with the organisers.) Topics of Interest ------------------ Topics of interest include, but are not limited to: * Standards, Technologies, Tools for the Semantic Web o Semantic Web standards (RDF, OWL, ...) o RDF/OWL, SKOS, .... and their applicability to bioinformatics o RDF Schemas and Query systems o Biomedical Ontologies and related tools o Formal approaches to large biomedical controlled terminologies and vocabularies * Systems for a Semantic Web for Bioinformatics o Bio-ontologies, RDF stores, Semantic Web Services o RDF repositories and query systems for life sciences o Semantically aware biomedical Web Services o Semantic Biological Data Integration Systems * Existing and perspective applications of the Semantic Web for Bioinformatics o Semantic browsers, Semantic collaborative research o Case studies, use cases, and scenarios o Semantic Web applications in life sciences Type of contributions ---------------------- The following possible original contributions are sought: * Oral communications (regular papers) * Posters * Software demos All accepted oral communications and posters will be published with the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). Furthermore, a selection of papers will be published in a special issue of the BMC Bioinformatics journal devoted to the SWAT4LS workshop. To this end, a special Call will be launched shortly after the workshop, for extended and revised versions of contributions submitted to the workshop and accepted either as oral communication or poster. Workshop Chairs ---------------- + Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, United Kingdom + Adrian Paschke, Biotechnology Centre, TU Dresden, Dresden, Germany + Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy + Andrea Splendiani, Medical Informatics Department, University of Rennes 1, Rennes, France ===================================================================== In Co-operation with: - National Cancer Research Institute, Genova, Italy - Biotechnology Centre, TU Dresden, Dresden, Germany - School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, United Kingdom - Universit? de Rennes 1, Rennes, France - e-Science Institute, Edinburgh, Scotland, United Kingdom - SeaLife Project, European Commission Information Society and Media - Laboratory for Interdisciplinary Technologies in Bioinformatics (LITBIO), Italy ===================================================================== For any information, refer to info at swat4ls.org . Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From quwubin at gmail.com Mon Sep 8 13:59:57 2008 From: quwubin at gmail.com (Wubin Qu) Date: Mon, 8 Sep 2008 21:59:57 +0800 Subject: [Biopython-announce] BioPythonGUI: Graphical User Interface for BioPython Message-ID: Hi all, I started a new project named BioPythonGUI for a few of days. The following is the 'About' page from BioPythonGUI project. BioPythonGUI is a Graphical User Interface of BioPython. BioPython is a widely used python module set in bioinformatics. It help researchers: - Parsing files in di fferent database formats - Interfaces into programs like Blast, Entrez and PubMed - A sequence class (can transcribe, translate, invert, etc) - Code for handling alignments of sequences - Clustering algorithms - etc. However, it's not everyone can use the BioPython, especially ones who do not know much about the programming. How can you expect a professor who never known about any programming to use BioPython to parse the BLAST report file? This is the problem which the BioPythonGUI would solve. I started the project with the goal "Everyone can use BioPython with BioPythonGUI". Until now, there are two modules SeqGUI and BlastGUI are available in BioPythonGUI. I would greatly appreciate if you use BioPythonGUI and send me the feedback. Please see the developer's blog for details. Project Blog: http://biopythongui.blogspot.com/ Download: https://sites.google.com/site/biopythongui/download Screenshots: http://picasaweb.google.com/quwubin/BioPythonGUI02# ______________________________ Best regards, Wubin Qu From mjldehoon at yahoo.com Wed Sep 10 14:14:49 2008 From: mjldehoon at yahoo.com (Michiel de Hoon) Date: Wed, 10 Sep 2008 07:14:49 -0700 (PDT) Subject: [Biopython-announce] Biopython 1.48 released Message-ID: <701345.92946.qm@web62402.mail.re1.yahoo.com> We are pleased to announce the release of Biopython 1.48. Some new functionality has been added, a few bugs have been fixed, the documentation has been updated, plus several obsolete modules have been deprecated (or explicitly labelled as obsolete). The following additional file formats are now supported in Bio.SeqIO and Bio.AlignIO: * reading and writing "tab" format (simple tab separated) * writing "nexus" files * reading "pir" files (NBRF/PIR) * basic support for writing "genbank" files (GenBank plain text) This release also fixes some problems reading Clustal alignments (introduced in Biopython 1.46 when consolidating Bio.AlignIO and Bio.Clustalw), and some updates to the Bio.Sequencing parsers. The SeqRecord and Alignment objects have a new method to get the object as a string in a given file format (handled via Bio.SeqIO and Bio.AlignIO). Bio.PubMed and the online code in Bio.GenBank are now considered obsolete, and we intend to deprecate them after the next release. For accessing PubMed and GenBank, please use Bio.Entrez instead. Martel and Bio.Mindy are now considered to be obsolete, and are likely to be deprecated and removed in a future release, at which point we will drop the optional dependency on mxTextTools. Bio.Fasta is also considered to be obsolete, please use Bio.SeqIO instead. We do intend to deprecate this module eventually, however, for several years this was the primary FASTA parsing module in Biopython and is likely to be in use in many existing scripts. In addition a number of other modules have been deprecated, including: Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics - see the DEPRECATED file for full details. Source distributions are available from the Biopython website at http://biopython.org, and Windows installers will be added shortly. My thanks to all bug reporters, code contributors and others who made this new release possible. Peter, on behalf of the Biopython developers P.S. This message will be forwarded to the Biopython anoucement mailing list shortly. For those of you who prefer news readers to email lists, have a look at the OBF news server: http://news.open-bio.org/news/2008/09/biopython-release-148/ where there are Biopython news feeds available: http://news.open-bio.org/news/category/obf-projects/biopython/feed/rdf http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss http://news.open-bio.org/news/category/obf-projects/biopython/feed/rss2 http://news.open-bio.org/news/category/obf-projects/biopython/feed/atom From paolo.romano at istge.it Tue Sep 16 14:12:12 2008 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 16 Sep 2008 14:12:12 -0000 Subject: [Biopython-announce] CFP: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) Message-ID: <200809161414.m8GEEBou051606@ibm43p.biotech.ist.unige.it> Apologies, if you're receiving multiple copies. ---------------------------------------------------------------- International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 28th November 2008, Edinburgh, UK http://www.swat4ls.org/ CALL FOR PAPERS Overview -------- The workshop is organized in sessions and open discussions. Invited speakers will present state-of-the-art, provocative lectures on the workshop's main topic, while a number of submissions will be accepted as oral presentations and posters on all workshop's topics. Workshop Description -------------------- Semantic Web technologies, tools and applications are starting to emerge in Life Sciences. In recent years, systems have been introduced and an increasing interest among researchers is arising. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences. Keynote Speakers ------------------------ + Semantic web technology in translational cancer research, Michael Krauthammer, Department of Pathology, Yale University School of Medicine, USA + Using Ontologies to bring Web Services on to the Semantic Web Mark Wilkinson, Dept. of Medical Genetics, University of British Columbia, Canada Workshop Venue and Format ------------------------ The workshop will take place in Edinburgh, Scotland, on 28 November 2008, and is hosted by the e-Science Institute of the UK's National e-Science Centre (NeSC). SWAT4LS will be a one-day workshop and will consist of two invited talks, regular paper and poster presentations. The workshop will conclude with a panel discussion on the strength and weaknesses of the Semantic Web for the Life Sciences. Deadlines --------- * Submission deadline (both papers and posters): 30 September 2008 * Notification of acceptance: 20 October 2008 * Camera-ready submission: 3 November 2008 (Authors who are interested in submitting a paper/poster to the workshop, but may require a short extension to the deadline, should get in touch with the organisers.) Topics of Interest ------------------ Topics of interest include, but are not limited to: * Standards, Technologies, Tools for the Semantic Web o Semantic Web standards (RDF, OWL, ...) o RDF/OWL, SKOS, .... and their applicability to bioinformatics o RDF Schemas and Query systems o Biomedical Ontologies and related tools o Formal approaches to large biomedical controlled terminologies and vocabularies * Systems for a Semantic Web for Bioinformatics o Bio-ontologies, RDF stores, Semantic Web Services o RDF repositories and query systems for life sciences o Semantically aware biomedical Web Services o Semantic Biological Data Integration Systems * Existing and perspective applications of the Semantic Web for Bioinformatics o Semantic browsers, Semantic collaborative research o Case studies, use cases, and scenarios o Semantic Web applications in life sciences Type of contributions ---------------------- The following possible original contributions are sought: * Oral communications (regular papers) * Posters * Software demos All accepted oral communications and posters will be published with the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). Furthermore, a selection of papers will be published in a special issue of the BMC Bioinformatics journal devoted to the SWAT4LS workshop. To this end, a special Call will be launched shortly after the workshop, for extended and revised versions of contributions submitted to the workshop and accepted either as oral communication or poster. Workshop Chairs ---------------- + Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, United Kingdom + Adrian Paschke, Biotechnology Centre, TU Dresden, Dresden, Germany + Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy + Andrea Splendiani, Medical Informatics Department, University of Rennes 1, Rennes, France ===================================================================== In Co-operation with: - National Cancer Research Institute, Genova, Italy - Biotechnology Centre, TU Dresden, Dresden, Germany - School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, United Kingdom - Universit? de Rennes 1, Rennes, France - e-Science Institute, Edinburgh, Scotland, United Kingdom - SeaLife Project, European Commission Information Society and Media - Laboratory for Interdisciplinary Technologies in Bioinformatics (LITBIO), Italy ===================================================================== For any information, refer to info at swat4ls.org . Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295