Peter Cock | 26 Apr 00:01 2016
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[Biopython] Community help needed to verify checksums for past releases

Dear Biopython developers,

Thank you to everyone who has helped with the website
migration to GitHub - I think this has gone pretty well overall:

https://biopython.org

The good news is the new GitHub Pages website seems to
be working nicely, and during this we've updated a lot of older
content. While there is still lots to fine tune, for me this is the
biggest remaining issue:

*Providing all the past releases via GitHub Pages*
https://github.com/biopython/biopython.github.io/issues/7

The sudden Biopython website migration was forced by the old
server failing after it was hacked to host spam advertising.
I would like your help here with verifying the checksums of our
past releases before putting them back online - just in case any
of the files rescued from the old server were corrupted when it
was hacked to host spam adverts. All the files checked so far
are fine, so this is likely just me being paranoid.

If anyone has old cached Biopython files under their Downloads
folder etc, could you reply with their checksums please?

Linux,

shasum - a 256 ~/Downloads/biopython-*
md5sum ~/Downloads/biopython-*
(Continue reading)

Peter Cock | 13 Apr 13:08 2016
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[Biopython] Biopython.org live on GitHub Pages - please check your contributions

Dear all,

As announced last week, the old MediaWiki home page hosted
by the OBF on Amazon had failed and needed a server rebuild.
This prompted me to finish the trial migration to GitHub Pages
urgently, and this is now live at http://biopython.org

http://lists.open-bio.org/pipermail/biopython/2016-April/015909.html
http://lists.open-bio.org/pipermail/biopython/2016-April/015919.html

At this point there are various little things which need fixing, e.g.

https://github.com/biopython/biopython.github.io/issues

Some of you are itching to tackle these which is great, but I'd like to
allow a day or so to urge everyone to have a look at the contributors
listing where I tried to map the old MediaWiki accounts to GitHub:

https://github.com/biopython/biopython.github.io/issues/2
https://github.com/biopython/biopython.github.io/graphs/contributors

Please get in touch (ideally via the GitHub issue above, or by email)
ASAP if your name is missing, or worse I've wrongly linked your
GitHub account to an old wiki edit (you have been BCC'd here).

(Fixing the authorship of the changes would require re-writing the
git history, which is something best avoided for group projects)

Thanks,

(Continue reading)

medsubscriber | 8 Apr 00:28 2016

[Biopython] PubMed Updates

A group of physicians recently launched a new site that allows users to
stay on top of the latest research from PubMed. Medsubcriber.com allows
physicians to enter in their keywords, author names, titles, or any
other search query and their notification schedule. This service is 100%
free and is simple to use. Please check out http://medsubscriber.com/
and let us know what you think or what improvements we should make.

We are also adding clinicaltrials.gov as well as a few other sources. 
Our goal is to provide a free service that will help physicians, medical 
researchers and students stay on top of the latest medical advancements.

Best,
Steve
MedSubscriber.com
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Peter Cock | 7 Apr 12:28 2016
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[Biopython] Biopython website is down

Dear Biopythoneers,

I'm sorry to be the bearer of bad news:

We've got some problems on the main OBF web server, which has
been on AWS since 2012:

https://news.open-bio.org/2012/11/04/server-transition-to-aws/

This runs biopython.org, bioperl.org, biojava.org, biosql.org etc.
and will likely need a rebuild to get us back online again...

This will delay the planned Biopython 1.67 release - although we
could do it anyway on PyPI only, and share the Windows Installers
etc once the website is back?

Good news:

We'd already migrated the main OBF website www.open-bio.org
(aka www.obf.io) to a separately hosted MediaWiki site, and the OBF
news blog to a separately hosted WordPress site, news.open-bio.org
aka news.obf.io - so they are not affected.

Migration:

You may recall the AWS MediaWiki server would periodically fail
with a MySQL outage. Also we had some problems with the OpenID
authentication when Google dropped support for the legacy API.
In general keeping MediaWiki & WordPress up to date was a burden
and potential security problem.
(Continue reading)

[Biopython] ANN: LAST CALL for SciPy (Scientific Python) 2016 Conference Talk / Poster Proposals - Due Friday 4/1

**ANN: LAST CALL for SciPy 2016 Conference Talk / Poster Proposals (Scientific Computing with Python) - Final Deadline - Friday April 1st**

SciPy 2016, the 15th annual Scientific Computing with Python conference, will be held July 11-17, 2016 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 650 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 2 days of tutorials (July 11-12), 3 days of talks (July 13-15), and 2 days of developer sprints (July 16-17). More info is available on the conference website at http://scipy2016.scipy.org (where you can sign up for the mailing list); or follow <at> scipyconf on Twitter.  

 

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

**SUBMIT A SCIPY 2016 TALK / POSTER PROPOSAL - DUE APRIL 1, 2016*

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

Submissions for talks and posters are welcome on our website (http://scipy2016.scipy.org). In your abstract, please provide details on what Python tools are being employed, and how. The talk and poster submission deadline is March 25th, 2016

 

SciPy 2016 will include 3 major topic tracks and 8 mini-symposia tracks.

 

Major topic tracks include:

- Scientific Computing in Python

- Python in Data Science (Big data and not so big data)

- High Performance Computing

 

Mini-symposia will include the applications of Python in:

- Earth and Space Science

- Engineering

- Medicine and Biology

- Social Sciences

- Special Purpose Databases

- Case Studies in Industry

- Education

- Reproducibility

 

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

 

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

**SCIPY 2016 REGISTRATION IS OPEN**

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

Please register early. SciPy early bird registration until May 22, 2016. Register at http://scipy2016.scipy.org. Plus, enter our t-shirt design contest to win a free registration. (Send a vector art file to scipy <at> enthought.com by March 31 to enter).

 

Important dates:

April 1: Talk and Poster Proposals Due

May 11: Plotting Contest Submissions Due

Apr 22: Tutorials Announced

Apr 22: Financial Aid Submissions Due

May 4: Talk and Posters Announced

May 22: Early Bird Registration Deadline

Jul 11-12: SciPy 2016 Tutorials

Jul 13-15: SciPy 2016 General Conference

Jul 16-17: SciPy 2016 Sprints

 

We look forward to an exciting conference and hope to see you in Austin in July!

 

The Scipy 2016 Committee

http://scipy2016.scipy.org/

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Jeremy Chase | 18 Mar 04:52 2016
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[Biopython] Problems with Phylo/PAML/codeml.py in newer BioPython version

Hi everyone,

I recently began transitioning my analyses from a big computing cluster that currently has an older version of BioPython (1.59) to a local box that I've installed the newest version of BioPython on (1.66). Unfortunately, I'm now having some problems using codeml via Bio. I'm not sure if this is due to differences between the two versions or simply a problem with how I have things configured, and I was hoping someone might have an idea about how to go about figuring that out. Incidentally, the version of python is also different (2.7.3 on the cluster, 2.7.6 on the new system.) Here is the error message when I get when I call cml.run() via the same script that works fine on the other cluster:
Traceback (most recent call last):
  File "codemlscript.py", line 117, in <module>
    results = cml.run()
  File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/codeml.py", line 186, in run
    Paml.run(self, ctl_file, verbose, command)
  File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/_paml.py", line 145, in run
    stdout=subprocess.PIPE)
  File "/usr/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Thanks very much for taking the time to read.

Cheers!
Jeremy

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Sean Brimer | 16 Mar 21:33 2016
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[Biopython] Editing an Bio.Seq.Seq object

Hello Biopython users, 

I'm trying to create a script that will allow me to add 'N' to a final fasta of a template-guided assembly. I have already posted this question on BioStars and received some good feedback and with it I feel I'm 99% done with what I am trying to complete. 

I am using python3 and Biopython 1.66

The link to the BioStars post is here: https://www.biostars.org/p/179755/

The code seems to do fine on making a dictionary of the coverage file and then making a set containing only the "no coverage" areas. I can edit the fasta header information i.e. new id, new description however I am unable to make an editted version of the Seq object. I have tried using the str() function and the .tomutable() function in several ways but none of them seem to be giving me my expected output. I suspect the error is in how I'm trying to call/edit the Seq function but from the tutorial guide I'm not sure why it's not working. 

Any guidance would be appreciated.

Thank you, 
Sean

my code is below:

from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
from Bio import SeqIO
import argparse 
 
## this makes a dict of the samtools depth coverage input file of all the 0's
coverageDict = {}
 
## this loops over the input depth information and appends the dictionary with 
## a key,value as genome position, depth of coverage
coverage = open("/home/sbrimer/Desktop/Columbia ST/1819_1/coverage.txt","r")
for line in coverage:
    coverages = line.split("\t")
    coverageDict[coverages[1]] = coverages[2]
coverage.close()
 
## this should read in the sequence file as an oblect, change it to a mutable
## object, then anywhere the coverageDict value = 0. Replace that nt with "N"
 
missing = {index for index,value in coverageDict.items() if value == 0}
def filter_coverage(index,value):
    return 'N' if index in missing else value
 
newSeqRec = []
with open("newfile.fasta","w") as handle:
    for seq_record in SeqIO.parse("Salmonella enterica subsp.fasta","fasta"):
        refseq = seq_record.seq
        newSeq = "".join(filter_coverage(index,value) for index,value in enumerate(refseq.tomutable(), start=1))
        newSeqRec = SeqRecord(Seq(newSeq),id ="new_id", description = str(seq_record.description))
    SeqIO.write(newSeqRec, handle, "fasta")
handle.close()

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Lluís Revilla | 15 Mar 14:45 2016
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[Biopython] PSI-BLAST

Hello!

I am trying to perform online a PSI-BLAST. In the tutorial there isn't any example so looking on the help I found what I thought it was the way:

record = SeqIO.read("protein.fasta", format="fasta")
result_handle = NCBIWWW.qblast('blastp', 'nr', record.format("fasta"),
                                    service='psi')
blast_record = NCBIXML.read(result_handle)

However it returns a normal Blast record. But the object I get is not the "PSIBlast record " described on the tutorial with information about. I haven't found the way to set the number of round of the PSI-BLAST (neither in the NCBI help at http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html ). 


How can I do a PSI-BLAST? 

Many thanks,

Lluís
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Peter Cock | 2 Mar 10:41 2016
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[Biopython] Fwd: BOSC 2016 Call for Abstracts

Dear all,

As BOSC co-chair I would like to encourage you all to think about
attending BOSC 2016, and if you are working on your own open
source software for bioinformatics please consider submitting an
abstract. See the email below and:

http://news.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/

We'll discuss who could give the traditional Biopython Project Update
talk at BOSC this year on the biopython-dev mailing list.

Also, as a member of the Open Bioinformatics Foundation (OBF)
Board of Directors, I am delighted to let you know about the new
OBF Travel Fellowship which could be used to attend BOSC:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

In case you missed the earlier announcement last year, we finally
got rid of the paper forms for OBF membership, see:

http://news.open-bio.org/2015/12/10/online-membership-form/

Thank you,

Peter

[Biopython developer, BOSC co-chair, OBF Secretary, etc.]

---------- Forwarded message ----------
From: Peter Cock <p.j.a.cock <at> googlemail.com>
Date: Tue, Mar 1, 2016 at 5:56 PM
Subject: BOSC 2016 Call for Abstracts
To: bosc-announce <at> lists.open-bio.org
Cc: bosc-reviewers <at> lists.open-bio.org, "bosc <at> open-bio.org" <bosc <at> open-bio.org>

Call for Abstracts for the 17th Annual Bioinformatics Open Source
Conference (BOSC 2016), a Special Interest Group (SIG) of ISMB 2016.

Dates: July 8-9, 2016
Location: Orlando, FL
Web site: http://www.open-bio.org/wiki/BOSC_2016
Email: bosc <at> open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce
Twitter:  <at> OBF_BOSC and  <at> OBF_News

Important Dates:

 * Call for one-page abstracts opens: March 1, 2016
 * Abstract submission deadline: April 1, 2016
 * Travel fellowship application deadline: April 15, 2016
 * Authors notified: May 6, 2016
 * Codefest 2016: July 6-7, 2016, Orlando, FL (confirming venue)
 * BOSC 2016: July 8-9, 2016, Orlando, FL
 * ISMB 2016: July 8-12, 2016, Orlando, FL

The Bioinformatics Open Source Conference (BOSC) is run as a two-day
meeting before the annual ISMB conference. It is organized by the Open
Bioinformatics Foundation (OBF), a non-profit group dedicated to
promoting the practice and philosophy of open source software
development and open science within the biological research community.
BOSC offers a focused environment for developers and users to interact
and share ideas about standards; software development practices;
practical techniques for solving bioinformatics problems; and
approaches that promote open science and sharing of data, results and
software.

We welcome one-page abstracts on any topic of relevance to open source
bioinformatics and open science. Presentation formats are lightning
talks, longer talks, and/or posters. We plan to offer a limited number
of travel fellowships to help offset expenses for some accepted
speakers who would not otherwise be able to attend BOSC – please see
the OBF Travel Fellowship announcement for more information:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

Session topics include:
 * Open Science and Reproducible Research
 * Standards and Interoperability
 * Data Science
 * Visualization
 * Translational Bioinformatics
 * Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in helping to sponsor
BOSC 2016, please contact us! Sponsors in 2015 included Google,
GigaScience, Curoverse and Bina – we thank them for their support.

Please see http://www.open-bio.org/wiki/BOSC_Abstract_Submission for
abstract submission instructions,

Thank you,

BOSC 2016 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Brad Chapman, Christopher
Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather
Wiencko

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Melcher, Ulrich | 28 Feb 00:39 2016

[Biopython] Installing Biopython on Mac

 I need help interpreting the instruction "You will need to have installed Apple's XCode tools from the App Store …, and then the optional command line tools from within the XCode GUI's options menu." from http://biopython.org/wiki/Download
I have no trouble installing the Xcode package, but am unable to locate either the tools or the options menu. I am not a developer.
Ulrich Melcher
Regents & RJ Sirny Professor
Department of Biochemistry & Molecular Biology
Oklahoma State University

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[Biopython] ANN: SciPy (Scientific Python) 2016 Conference Call for Talk / Tutorial Proposals Open Until 3/25

**SciPy 2016 Conference (Scientific Computing with Python) Announcement**

 

*Call for Proposals: Submit Your Tutorial and Talk Ideas by March 25, 2015 at http://scipy2016.scipy.org.

 

SciPy 2016, the 15th annual Scientific Computing with Python conference, will be held July 11-17, 2016 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 650 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 2 days of tutorials (July 11-12), 3 days of talks (July 13-15), and 2 days of developer sprints (July 16-17). More info is available on the conference website at http://scipy2016.scipy.org (where you can sign up for the mailing list); or follow <at> scipyconf on Twitter.  

 

We hope you’ll join us - early bird registration is open until May 22, 2016 at http://scipy2016.scipy.org/ehome/146062/332936/?&&

 

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: http://scipy2016.scipy.org.

 

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

*SUBMIT A SCIPY 2016 TUTORIAL PROPOSAL - DUE MARCH 21, 2016*

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

Details and submission here: http://scipy2016.scipy.org/ehome/146062/332967/?&&

 

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 opportunityto share your knowledge and stipends are available.

 

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

**SUBMIT A SCIPY 2016 TALK / POSTER PROPOSAL - DUE MARCH 25, 2016*

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

Details and submission here: http://scipy2016.scipy.org/ehome/146062/332968/?&&

 

SciPy 2016 will include 3 major topic tracks and 8 mini-symposia tracks.

 

Major topic tracks include:

- Scientific Computing in Python

- Python in Data Science (Big data and not so big data)

- High Performance Computing


Mini-symposia will include the applications of Python in:


- Earth and Space Science

- Engineering

- Medicine and Biology

- Social Sciences

- Special Purpose Databases

- Case Studies in Industry

- Education

- Reproducibility

 

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

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

**SCIPY 2016 REGISTRATION IS OPEN**

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

Please register early. SciPy early bird registration until May 22, 2016! Register at http://scipy2016.scipy.org. Plus, enter our t-shirt design contest to win a free registration. (Send a vector art file to scipy <at> enthought.com by March 31 to enter).

 

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Gmane