Goutham atla | 29 Mar 20:09 2015
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[Biopython] Biopython genepop help

Dear All,

I am trying to use genePop module of Biopython. I am trying to create a Record object.

I am little bit confused as I did not find any examples on how to use Record class.

If I have a file named "test.genepop", how should I create a Record object out of that file ?

My ultimate goal is to replace 0000 0000 000 notation to some thing like 9 9 9 to indicate missing data. Is there any simpler way of doing it ?


Regards,
--
Goutham Atla
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Horea Christian | 28 Mar 23:20 2015
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[Biopython] Determine thermocycler sequence for PCR

Hi, do you guys know any good literature reference that provides a reliable equation to determine the ideal step temperatures and durations for a PCR given the primers and the amplicon?

I see annealing temps can be calculated with biopython via SeqUtils.MeltingTemp, which is nice, but it would be even greater if we could provide assistance with designing more of the PCR protocol. I am asking this also because I have a set of new primers over here which likely need a new thermocycler protocol, and all I found via google was very vague.

BEst,
Christian
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[Biopython] SciPy 2015 Call for Propsals & Registration Open - tutorial & talk submissions due April 1st - Life & Medical Sciences Mini-Symposia planned

Wanted to share the Call for Proposals and registration info about the 2015
SciPy Conference (below) - more info on the conference website at
http://scipy2015.scipy.org. Thought you might have some interesting
proposals for the computational life and medical sciences minisymposia?

Best regards, 

Courtenay Godshall
SciPy 2015 Communications Co-Chair

------------------

**SciPy 2015 Conference (Scientific Computing with Python) Call for
Proposals and Registration Open: Submit Your Tutorial and Talk Ideas by
April 1, 2015 at http://scipy2015.scipy.org.**  

SciPy 2015, the fourteenth annual Scientific Computing with Python
conference, will be held July 6-12, 2015 in Austin, Texas. SciPy is a
community dedicated to the advancement of scientific computing through open
source Python software for mathematics, science, and engineering. The annual
SciPy Conference brings together over 500 participants from industry,
academia, and government to showcase their latest projects, learn from
skilled users and developers, and collaborate on code development. The full
program will consist of two days of tutorials by followed by three days of
presentations, and concludes with two days of developer sprints. More info
available on the conference website at http://scipy2015.scipy.org; you can
also sign up on the website for mailing list updates or follow  <at> scipyconf on
Twitter. We hope you'll join us - early bird registration is open until May
15, 2015 at http://scipy2015.scipy.org 

We encourage you to submit tutorial or talk proposals in the categories
below; please also share with others who you'd like to see participate!
Submit via the conference website  <at>  http://scipy2015.scipy.org.

*SCIPY TUTORIAL SESSION PROPOSALS -  DEADLINE EXTENDED TO WED APRIL 1, 2015*
The SciPy experience kicks off with two days of tutorials. These sessions
provide extremely affordable access to expert training, and consistently
receive fantastic feedback from participants. We're looking for submissions
on topics from introductory to advanced - we'll have attendees across the
gamut looking to learn. Whether you are a major contributor to a scientific
Python library or an expert-level user, this is a great opportunity to share
your knowledge and stipends are available. Submit Your Tutorial Proposal on
the SciPy 2015 website: http://scipy2015.scipy.org

*SCIPY TALK AND POSTER SUBMISSIONS - DUE April 1, 2015* SciPy 2015 will
include 3 major topic tracks and 7 mini-symposia tracks. Submit Your Talk
Proposal on the SciPy 2015 website: http://scipy2015.scipy.org

Major topic tracks include:
- Scientific Computing in Python (General track)
- Python in Data Science
- Quantitative and Computational Social Sciences

Mini-symposia will include the applications of Python in:
- Astronomy and astrophysics
- Computational life and medical sciences
- Engineering
- Geographic information systems (GIS)
- Geophysics
- Oceanography and meteorology
- Visualization, vision and imaging

If you have any questions or comments, feel free to contact us at:
scipy-organizers <at> scipy.org.

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Alan | 17 Mar 16:44 2015
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[Biopython] 2 seqs in one Bio.SeqIO, is it possible?

My ultimate scope is to generate a XML file with two sequences: one protein sequence and one DNA sequence, like that:

<AAseq>XLLLAINGVTECFTFAAMS</AAseq>
<DNAseq>NTTCTCCTGCTTGCCATCAATGGAGTGACAGAGTGTTTCACATTTG</DNAseq>

But I am afraid that Bio.SeqIO can only keep one Seq object at a time per record.

Hoping that I am wrong, can some tell me how to do it?

a0 is my target record:

SeqRecord(seq=Seq('XLLLAINGVTECFTFAAMS', ProteinAlphabet()), id='sp|O07835|IORA_THEKO', name='sp|O07835|IORA_THEKO', description='sp|O07835|IORA_THEKO Indolepyruvate oxidoreductase subunit IorA OS=Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) GN=iorA PE=1 SV=2', dbxrefs=[])

and b0 is my source record, from which I only want the DNA sequence,  b0.seq = Seq('NTTCTCCTGCTTGCCATCAATGGAGTGAC...TTG', DNAAlphabet())

Any help would be very much appreciated.

Many thanks in advance,

Alan

--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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John DeFilippo | 15 Mar 01:54 2015
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[Biopython] Biopython 1.65 post-install test - get different result on one line

In Biopython Installation (http://biopython.org/DIST/docs/install/Installation.html)
#6 -  Making sure everything worked

5th line of python code
new_seq.translate()

gives output as
Seq('DQK', HasStopCodon(IUPACProtein(), '*’))

but I get
Seq('DQK', IUPACProtein())

Does this indicate something wrong with my install?

Thanks
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Horea Chrristian | 12 Mar 00:11 2015
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[Biopython] Why can I not access the mouse_genomic_transcript database with NCBIWWW?

Hi, I am trying to use NCBIWWW. I find it difficult to figure out what the possible database names are. I understand that this is where the NCBI BLAST databases are stored: ftp://ftp.ncbi.nlm.nih.gov/blast/db/

and some of those IDs work... But why for instance will mouse_genomic_transcript not work? the only other mouse alternative is mouse_est (which works), but that only gives me expressed genes - I'd like to use NCBI's BLAST against the whole mouse genome and only the mouse genome from biopython. Can I do this?

Many Thanks,
Christian
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Tommy Carstensen | 10 Mar 12:47 2015
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[Biopython] Fst calculation

Is it possible to calculate Fst with Biopython without installing the
Genepop module? I want to avoid too many module dependencies.
Otherwise I'll just do a vcftools or plink subprocess instead or write
the code myself. Thanks.
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Tommy Carstensen | 10 Mar 12:46 2015
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[Biopython] Fst calculation

Is it possible to calculate Fst with Biopython without installing the
Genepop module? I want to avoid too many module dependencies.
Otherwise I'll just do a vcftools or plink subprocess instead or write
the code myself. Thanks.
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Joshua Klein | 4 Mar 13:59 2015
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[Biopython] Glycoinformatics Library

Hello,

I'm working on a library for interacting with and manipulating glycomics data.

The library can currently do the following:
  1. Read and write GlycoCT Condensed format carbohydrate structures that are concrete (having no variable or undefined structures)
  2. Read GlycoCTXML format carbohydrate structures that are concrete
  3. Manipulate the tree structure, adding and removing monosaccharide and substituent nodes, as well as altering existing nodes and edges. 
  4. Calculate elemental compositions for glycan structures
  5. Create arbitrary chemical derivitizations (e.g. permethylation) of glycan structures
  6. Generate B, C, Y, and Z fragments from structures as observed when analyzing a structure with tandem mass spectrometry.
  7. Make API calls against GlycomeDB to download structures and annotations on the fly
  8. Perform sub-tree inclusion and maximum common substructure searches with fuzzy matching.
  9. Plot glycan structures using the Consortium for Functional Glycomics symbol nomenclature with matplotlib.
  10. Perform error tolerant name inference on monosaccharides
The library is a work in progress still. The code is hosted at https://github.com/mobiusklein/pygly2

Is there any interest in these (or related) features in the community?

The library is self-contained, having not dependencies on Biopython currently. Is there any interest in the community in seeing a common API written to include with Biopython?

Thank you,
Joshua Klein
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Alexey Morozov | 4 Mar 07:12 2015
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[Biopython] Reading from binary BLAST db

Is there any support for compiled BLAST databases (*.pin/*.phr/*.psq) I/O in biopython? I need to get complete sequences that match, not just hsps that Bio.Blast.NCBIXML can read.

--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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Peter Cock | 3 Mar 16:50 2015

[Biopython] Sadly OBF not accepted for GSoC 2015

This announcement was posted to the OBF blog here:
http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/

Dear all,

Last year’s Google Summer of Code 2014 was very productive for the OBF
with six students working on Bio* and related bioinformatics projects
[1]. We applied to be part of GSoC 2015, but unfortunately this year
were not accepted.

Google’s program is enormously popular, and over-subscribed, meaning
Google has had to rotate organisation membership. The OBF is grateful
to have been accepted in 2010, 2011, 2012 and 2014. This year any
participation will be down to individual projects to find a willing
umbrella group from the organisations accepted for GSoC 2015 [2]. For
example, a Biopython project was included under NESCent for GSoC 2013.

Other organizations with bioinformatics as keyword are Ruby Science
Foundation, Department of Biomedical Informatics, Stony Brook
University, OncoBlocks, University of Nebraska – Helikar Lab. Other
organizations related to sciences are ASCEND , BRL-CAD, Debian Project
, HPCC Systems®,  International Neuroinformatics Coordinating
Facility, lmonade: scientific software distribution, OSGeo – Open
Source Geospatial Foundation, The Concord Consortium, The
Visualization Toolkit. Languages: Python, Scala, Apache Foundation.
Last but not least : Global Alliance for Genomics & Health. [3]

On behalf of the OBF, we would like to thank our volunteer GSoC
Administrators, Raoul Bonnal and Francesco Strozzi, for organising our
application - and all our potential mentors across the Bio* projects
who put forward potential project suggestions.

Peter
OBF Secretary

[1] http://news.open-bio.org/news/2015/02/obf-gsoc-2014-wrapup/
[2] https://www.google-melange.com/gsoc/org/list/public/google/gsoc2015
[3] See links on
http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/

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Gmane