From p.j.a.cock at googlemail.com Tue Feb 5 17:05:25 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 5 Feb 2013 22:05:25 +0000 Subject: [Biopython-announce] Biopython 1.61 released Message-ID: Dear Biopythoneers, Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). The updated Biopython Tutorial and Cookbook is online (PDF). Platforms/Deployment: We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). We are still encouraging early adopters to help test on these platforms, and have included a ?beta? installer for Python 3.2 (and Python 3.3 to follow soon) under 32-bit Windows. Please note we are phasing out support for Python 2.5. We will continue support for at least one further release (Biopython 1.62). This could be extended given feedback from our users. Focusing on Python 2.6 and 2.7 only will make writing Python 3 compatible code easier. New Features: GenomeDiagram has three new sigils (shapes to illustrate features). OCTO shows an octagonal shape, like the existing BOX sigil but with the corners cut off. JAGGY shows a box with jagged edges at the start and end, intended for things like NNNNN regions in draft genomes. Finally BIGARROW is like the existing ARROW sigil but is drawn straddling the axis. This is useful for drawing vertically compact figures where you do not have overlapping genes. New module Bio.Graphics.ColorSpiral can generate colors along a spiral path through HSV color space. This can be used to make arbitrary ?rainbow? scales, for example to color features or cross-links on a GenomeDiagram figure. The Bio.SeqIO module now supports reading sequences from PDB files in two different ways. The ?pdb-atom? format determines the sequence as it appears in the structure based on the atom coordinate section of the file (via Bio.PDB, so NumPy is currently required for this). Alternatively, you can use the ?pdb-seqres? format to read the complete protein sequence as it is listed in the PDB header, if available. The Bio.SeqUtils module how has a seq1 function to turn a sequence using three letter amino acid codes into one using the more common one letter codes. This acts as the inverse of the existing seq3 function. The multiple-sequence-alignment object used by Bio.AlignIO etc now supports an annotation dictionary. Additional support for per-column annotation is planned, with addition and splicing to work like that for the SeqRecord per-letter annotation. The Bio.Motif module has been updated and reorganized. To allow for a clean deprecation of the old code, the new motif code is stored in a new module Bio.motifs, and a PendingDeprecationWarning was added to Bio.Motif. Experimental Code ? SearchIO: This release also includes Bow?s Google Summer of Code work writing a unified parsing framework for NCBI BLAST (assorted formats including tabular and XML), HMMER, BLAT, and other sequence searching tools. This is currently available with the new BiopythonExperimentalWarning to indicate that this is still somewhat experimental. We?re bundling it with the main release to get more public feedback, but with the big warning that the API is likely to change. In fact, even the current name of Bio.SearchIO may change since unless you are familiar with BioPerl its purpose isn?t immediately clear. Contributors: Brandon Invergo Bryan Lunt (first contribution) Christian Brueffer (first contribution) David Cain Eric Talevich Grace Yeo (first contribution) Jeffrey Chang Jingping Li (first contribution) Kai Blin (first contribution) Leighton Pritchard Lenna Peterson Lucas Sinclair (first contribution) Michiel de Hoon Nick Semenkovich (first contribution) Peter Cock Robert Ernst (first contribution) Tiago Antao Wibowo ?Bow? Arindrarto Thank you all. Release announcement here (RSS feed available): http://news.open-bio.org/news/2013/02/biopython-1-61-released/ P.S. You can follow @Biopython on Twitter https://twitter.com/Biopython From p.j.a.cock at googlemail.com Thu Feb 7 06:33:25 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 7 Feb 2013 11:33:25 +0000 Subject: [Biopython-announce] Biopython 1.61 released In-Reply-To: References: Message-ID: On Tue, Feb 5, 2013 at 10:05 PM, Peter Cock wrote: > Dear Biopythoneers, > > Source distributions and Windows installers for Biopython 1.61 are now > available from the downloads page on the Biopython website and from > the Python Package Index (PyPI). > > The updated Biopython Tutorial and Cookbook is online (PDF). > > Platforms/Deployment: > > We currently support Python 2.5, 2.6 and 2.7 and also test under > Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython > 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C > extensions). We are still encouraging early adopters to help test on > these platforms, and have included a ?beta? installer for Python 3.2 > (and Python 3.3 to follow soon) under 32-bit Windows. For those of you wanting to try Biopython on Python 3.3 on Windows, there is now an installer for Biopython 1.61 built against NumPy 1.7.0rc2. NumPy 1.7 is their first release to support Python 3.3, and the official release is expected to be near-identical to this second release candidate, see: http://mail.scipy.org/pipermail/numpy-discussion/2013-February/065384.html Regards, Peter From p.j.a.cock at googlemail.com Wed Feb 27 17:32:35 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 27 Feb 2013 22:32:35 +0000 Subject: [Biopython-announce] Fwd: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts In-Reply-To: References: Message-ID: The new bioinformatics mini-symposium this year makes SciPy 2013 especially interesting. Peter ---------- Forwarded message ---------- From: *Jonathan Rocher* Date: Wednesday, February 27, 2013 Subject: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts To: SciPy Users List , numfocus at googlegroups.com, Discussion of Numerical Python [Apologies for cross-posts] Dear all, The annual SciPy Conference (Scientific Computing with Python) allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. *The deadline for abstract submissions is March 20th, 2013. * Submissions are welcome that address general Scientific Computing with Python, one of the two special themes for this years conference (machine learning & reproducible science), or the domain-specific mini-symposiaheld during the conference (Meteorology, climatology, and atmospheric and oceanic science, Astronomy and astrophysics, Medical imaging, Bio-informatics). Please submit your abstract at the SciPy 2013 website abstract submission form . Abstracts will be accepted for posters or presentations. Optional papers to be published in the conference proceedings will be requested following abstract submission. This year the proceedings will be made available prior to the conference to help attendees navigate the conference. We look forward to an exciting and interesting set of talks, posters, and discussions and hope to see you at the conference. The SciPy 2013 Program Committee Chairs Matt McCormick, Kitware, Inc. Katy Huff, University of Wisconsin-Madison and Argonne National Laboratory From chapmanb at 50mail.com Thu Feb 28 21:36:34 2013 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 28 Feb 2013 21:36:34 -0500 Subject: [Biopython-announce] [ANN] SciPy2013: Call for abstracts In-Reply-To: References: Message-ID: <87ppzjsv65.fsf@fastmail.fm> Peter; Thanks for sending this out. I'm helping with the organization of the SciPy bioinformatics session thanks to Peter's recommendation and wrote up a little bit about the types of abstracts that would fit will with the overall theme of SciPy: http://j.mp/Z4xxXB This is a great chance to connect with another open source scientific community so definitely send in an abstract if this is of interest; the deadline is coming up next month: March 20th. Austin also has awesome music and barbecue in addition to science and hacking so lots of reasons to attend, Brad > The new bioinformatics mini-symposium this year makes SciPy 2013 > especially interesting. > > Peter > > ---------- Forwarded message ---------- > From: *Jonathan Rocher* > Date: Wednesday, February 27, 2013 > Subject: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts > To: SciPy Users List , numfocus at googlegroups.com, > Discussion of Numerical Python > > > [Apologies for cross-posts] > > Dear all, > > The annual SciPy Conference (Scientific Computing with > Python) allows > participants from academic, commercial, and governmental organizations to > showcase their latest projects, learn from skilled users and developers, > and collaborate on code development. *The deadline for abstract submissions > is March 20th, 2013. * > > Submissions are welcome that address general Scientific Computing with > Python, one of the two special themes for this years conference (machine > learning & reproducible science), or the domain-specific > mini-symposiaheld > during the conference (Meteorology, climatology, and atmospheric and > oceanic science, Astronomy and astrophysics, Medical imaging, > Bio-informatics). > > Please submit your abstract at the SciPy 2013 website abstract submission > form . > Abstracts will be accepted for posters or presentations. Optional papers to > be published in the conference proceedings will be requested following > abstract submission. This year the proceedings will be made available prior > to the conference to help attendees navigate the conference. > > We look forward to an exciting and interesting set of talks, posters, and > discussions and hope to see you at the conference. > The SciPy 2013 Program Committee Chairs > > Matt McCormick, Kitware, Inc. > Katy Huff, University of Wisconsin-Madison and Argonne National Laboratory > _______________________________________________ > Biopython mailing list - Biopython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython From p.j.a.cock at googlemail.com Tue Feb 5 22:05:25 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 5 Feb 2013 22:05:25 +0000 Subject: [Biopython-announce] Biopython 1.61 released Message-ID: Dear Biopythoneers, Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). The updated Biopython Tutorial and Cookbook is online (PDF). Platforms/Deployment: We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). We are still encouraging early adopters to help test on these platforms, and have included a ?beta? installer for Python 3.2 (and Python 3.3 to follow soon) under 32-bit Windows. Please note we are phasing out support for Python 2.5. We will continue support for at least one further release (Biopython 1.62). This could be extended given feedback from our users. Focusing on Python 2.6 and 2.7 only will make writing Python 3 compatible code easier. New Features: GenomeDiagram has three new sigils (shapes to illustrate features). OCTO shows an octagonal shape, like the existing BOX sigil but with the corners cut off. JAGGY shows a box with jagged edges at the start and end, intended for things like NNNNN regions in draft genomes. Finally BIGARROW is like the existing ARROW sigil but is drawn straddling the axis. This is useful for drawing vertically compact figures where you do not have overlapping genes. New module Bio.Graphics.ColorSpiral can generate colors along a spiral path through HSV color space. This can be used to make arbitrary ?rainbow? scales, for example to color features or cross-links on a GenomeDiagram figure. The Bio.SeqIO module now supports reading sequences from PDB files in two different ways. The ?pdb-atom? format determines the sequence as it appears in the structure based on the atom coordinate section of the file (via Bio.PDB, so NumPy is currently required for this). Alternatively, you can use the ?pdb-seqres? format to read the complete protein sequence as it is listed in the PDB header, if available. The Bio.SeqUtils module how has a seq1 function to turn a sequence using three letter amino acid codes into one using the more common one letter codes. This acts as the inverse of the existing seq3 function. The multiple-sequence-alignment object used by Bio.AlignIO etc now supports an annotation dictionary. Additional support for per-column annotation is planned, with addition and splicing to work like that for the SeqRecord per-letter annotation. The Bio.Motif module has been updated and reorganized. To allow for a clean deprecation of the old code, the new motif code is stored in a new module Bio.motifs, and a PendingDeprecationWarning was added to Bio.Motif. Experimental Code ? SearchIO: This release also includes Bow?s Google Summer of Code work writing a unified parsing framework for NCBI BLAST (assorted formats including tabular and XML), HMMER, BLAT, and other sequence searching tools. This is currently available with the new BiopythonExperimentalWarning to indicate that this is still somewhat experimental. We?re bundling it with the main release to get more public feedback, but with the big warning that the API is likely to change. In fact, even the current name of Bio.SearchIO may change since unless you are familiar with BioPerl its purpose isn?t immediately clear. Contributors: Brandon Invergo Bryan Lunt (first contribution) Christian Brueffer (first contribution) David Cain Eric Talevich Grace Yeo (first contribution) Jeffrey Chang Jingping Li (first contribution) Kai Blin (first contribution) Leighton Pritchard Lenna Peterson Lucas Sinclair (first contribution) Michiel de Hoon Nick Semenkovich (first contribution) Peter Cock Robert Ernst (first contribution) Tiago Antao Wibowo ?Bow? Arindrarto Thank you all. Release announcement here (RSS feed available): http://news.open-bio.org/news/2013/02/biopython-1-61-released/ P.S. You can follow @Biopython on Twitter https://twitter.com/Biopython From p.j.a.cock at googlemail.com Thu Feb 7 11:33:25 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 7 Feb 2013 11:33:25 +0000 Subject: [Biopython-announce] Biopython 1.61 released In-Reply-To: References: Message-ID: On Tue, Feb 5, 2013 at 10:05 PM, Peter Cock wrote: > Dear Biopythoneers, > > Source distributions and Windows installers for Biopython 1.61 are now > available from the downloads page on the Biopython website and from > the Python Package Index (PyPI). > > The updated Biopython Tutorial and Cookbook is online (PDF). > > Platforms/Deployment: > > We currently support Python 2.5, 2.6 and 2.7 and also test under > Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython > 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C > extensions). We are still encouraging early adopters to help test on > these platforms, and have included a ?beta? installer for Python 3.2 > (and Python 3.3 to follow soon) under 32-bit Windows. For those of you wanting to try Biopython on Python 3.3 on Windows, there is now an installer for Biopython 1.61 built against NumPy 1.7.0rc2. NumPy 1.7 is their first release to support Python 3.3, and the official release is expected to be near-identical to this second release candidate, see: http://mail.scipy.org/pipermail/numpy-discussion/2013-February/065384.html Regards, Peter From p.j.a.cock at googlemail.com Wed Feb 27 22:32:35 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 27 Feb 2013 22:32:35 +0000 Subject: [Biopython-announce] Fwd: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts In-Reply-To: References: Message-ID: The new bioinformatics mini-symposium this year makes SciPy 2013 especially interesting. Peter ---------- Forwarded message ---------- From: *Jonathan Rocher* Date: Wednesday, February 27, 2013 Subject: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts To: SciPy Users List , numfocus at googlegroups.com, Discussion of Numerical Python [Apologies for cross-posts] Dear all, The annual SciPy Conference (Scientific Computing with Python) allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. *The deadline for abstract submissions is March 20th, 2013. * Submissions are welcome that address general Scientific Computing with Python, one of the two special themes for this years conference (machine learning & reproducible science), or the domain-specific mini-symposiaheld during the conference (Meteorology, climatology, and atmospheric and oceanic science, Astronomy and astrophysics, Medical imaging, Bio-informatics). Please submit your abstract at the SciPy 2013 website abstract submission form . Abstracts will be accepted for posters or presentations. Optional papers to be published in the conference proceedings will be requested following abstract submission. This year the proceedings will be made available prior to the conference to help attendees navigate the conference. We look forward to an exciting and interesting set of talks, posters, and discussions and hope to see you at the conference. The SciPy 2013 Program Committee Chairs Matt McCormick, Kitware, Inc. Katy Huff, University of Wisconsin-Madison and Argonne National Laboratory