Thomas Girke | 22 Oct 19:09 2014

[Biopython] Faculty Position in Computational Systems Biology at UC Riverside

University of California, Riverside
AP Recruit job link:

We are seeking an Assistant Professor in the field of Computational
Systems Biology. Research should be in systems biology, using
computational approaches or a combination of both experimental and
computational approaches.

Assistant Professor. Appointment and salary will be competitive and
commensurate with accomplishments.

University of California, Riverside.

The successful candidate will hold an academic appointment in the
Department of Botany and Plant Sciences with the option of a secondary
cooperating faculty appointment in a quantitative department such as
statistics, computer science, engineering or related. The candidate will
also join the innovative and multidisciplinary Institute for Integrative
Genome Biology (IIGB) which connects theoretical and experimental
researchers from different departments in Life, Physical and
Mathematical Sciences, Medicine, Engineering and various campus based
Centers. The IIGB is organized around a 10,000 sq.ft. suite of
Instrumentation Facilities that serve as a centralized, shared­use
resource for faculty, staff and students, offering advanced tools in
bioinformatics, microscopy, proteomics and genomics. Its bioinformatic
component is equipped with a modern high­performance compute (HPC)
(Continue reading)

Ivan Gregoretti | 21 Oct 22:56 2014

[Biopython] Unix pipes and APIs like NcbiblastxCommandline()

Hello everybody

Can somebody suggest a way to run an API like NcbiblastxCommandline()
but directing the output to standard output?

For instance, this is the conventional execution with output directed
to a file, in this case opuntia.csv:

from Bio.Blast.Applications import NcbiblastxCommandline
blastx_cline = NcbiblastxCommandline("/mnt/shared/ncbi-blast-2.2.29+/blastx",
query="opuntia.fasta", db="nr", evalue=0.001, outfmt=10,

Now, what I would like to know is how to run this API with something like

out="/dev/stdout" instead of out="opuntia.csv".

In other words, I seek to avoid the creation of opuntia.csv.

Optional context:

I can currently execute local blast from within Python and direct its
output to a pipe (i.e. subprocess.Popen...). I am now interested in
trying the API way as it is likely to be more robust than my
implementation and already tested by a very large number of users.

Thank you,


(Continue reading)

Ivan Gregoretti | 20 Oct 21:08 2014

[Biopython] Running a specific version of NCBI BLAST from within Biopython

Hello Biopythoneers,

I have multiple versions of NCBI BLAST installed in my Linux box. I
need them all.

How do I tell Biopython which version of local BLAST I want to run each time?

Is it possible to specify the path to the desired executable?

Thank you,


Ivan Gregoretti, PhD
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Jaime Tovar | 17 Oct 15:05 2014

[Biopython] Using Phylo to draw trees with images in nodes

Hi all,

Sorry, seems my google fu is low today. Have been trying to find 
information about a way to add small images next to the species names in 
trees generated with Biopython/Phylo. But I'm not even sure it is 
possible. I want to do something in the likes of trees produced with 
ETE2. I can't use ETE2 because of problems with the dependencies :(.

Thanks in advance for any help!

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Mario Pavone | 17 Oct 12:49 2014

[Biopython] 1st announcement: Synthetic and Systems Biology Summer School: Biology meets Engineering and Computer Science, Taormina - Sicily, Italy July 5-9, 2015

Call for Participation (apologies for multiple copies)

Synthetic and Systems Biology Summer School: Biology meets Engineering  
and Computer Science - 2nd Edition
Taormina - Sicily, Italy, July 5-9, 2015 <at>

** Deadlines **
Student Application: February 15, 2015
Oral/Poster Submission: February 15, 2015

The Synthetic and Systems Biology Summer School (SSBSS) is a  
full-immersion course on cutting-edge advances in systems and  
synthetic biology with lectures delivered by world-renowned experts.  
The school provides a stimulating environment for doctoral students,  
early career researches and industry leaders. Participants will also  
have the chance to present their results (Oral presentations or  
Posters) and to interact with their peers.

** Topics **
Genetic Engineering
Metabolic Engineering
Genome Design
Reading and Writing Genomes
Pathway Design
(Continue reading)

Ivan Erill | 15 Oct 22:14 2014

[Biopython] WP_XXXXXXX RefSeq records

For bacteria, NCBI RefSeq is progressively adopting the non-redundant protein sequence standard. These protein records are aggregates for any bacterial genes coding for the same exact coding region (a "detailed" description of the implementation can be found here (

Essentially, all traditional NP_XXXXXXX and YP_XXXXXXX protein records in bacteria RefSeq now map to a unique WP_XXXXXXX record. While this is possibly a good idea, it can create problems if one is trying to get back to (at least one of) the nucleotide sequence coding for the WP_XXXXXXX record.

For NP_XXXXXXX and YP_XXXXXXX records, one can easily fetch the protein record with Entrez.efetch, and then use the GB "coded_by" qualifier to access the corresponding nucleotide record.

Per specification of the new WP format:
- WP_ records will not include information about the corresponding Nucleotide sequences
on the sequence record.
- WP_ records will have links to Nucleotide in the Related Information section of the page display. Links in this section are available through NCBI’s E-utilities API.

I have been trying, unsuccessfully, to access the nucleotide record for WP_ proteins using Entrez.elink.

Here is an example:

Clicking on "Genomic records" in "Related information" will bring up the GenBank record containing the CDS for this protein, but I have been unable to use Entrez.elink to get to the information on the "Related information" panel. If I query:

handle = Entrez.elink(dbfrom="protein", id="653545797")

I essentially get an empty LinkSetDb. Any clues?

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Trevor Bell | 15 Oct 17:00 2014

[Biopython] Original BLAST query

I have run stand-alone BLAST of query sequences (Q1, Q2, Q3) against a set of reference sequences and written the results out in XML format, which I am then processing via BioPython. I am unable to find the original query sequences (Q1, Q2, Q3) in the XML file. Is this correct? When comparing each set of BLAST results, it would be useful to have access to the original query sequence, which was subjected to the BLAST, but this does not appear to be stored in the XML output.
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Naman Bhayani | 12 Oct 22:06 2014

[Biopython] Need Guidance to start contributing to BioPython

Hello sir,
 I am Naman,i study EEE,2nd year at BITS Pilani.
 I am relatively new to opensource contribution.I have started contributing since a few days and i am actively contributing BinPy organisation,and it participated in gsoc  2014.

My Github Profile:

My skills:C,C++,Python,Basic web development.
I am also interested in biology,so i thought it would be nice to explore and contribute to this organisation
I am willing to learn a lot more things.

Please tell me what do i need to know to start contributing to biopython and how should i begin contributing?

Thank you very much
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Andreas Prlic | 7 Oct 20:52 2014

[Biopython] The NIH Software Discovery Index | We invite your comments -- a system for linking software, publications and users in the research community.

Greetings Everyone,


On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported meeting that focused on the opportunities and challenges of developing a software management ecosystem that could be valuable for finding and linking software, publications and users in the research community. You may be also be aware of a related project, the Data Discovery Index, which will be fully integrated with the software system.

The product of this workshop and the subsequent discussion is a document which details the opportunities and challenges of developing a Software Discovery Index that would enable researchers to find, cite, and link software and analysis tools publications and researchers. To ensure that the opportunities, challenges, and recommendations detailed in the document reflect the breadth of experience from the community, we are seeking your input.  In conjunction with related efforts already under way at NIH, including the development of a Data Discovery Index, the final document will be used by the NIH Office of the Associate Director (ADDS) to inform a strategy for the development of a Software Discovery Index and a commons ecosystem for data, software, and resources.


We need your help to ensure that this critical task is achieved: to guide the development of a community based system that gives credit and acknowledgment to the builder and maintainers of the software we all depend on! We invite all users, software developers, publishers, and software repository administrators to review our report prior to its submission to the NIH. Please complete your review and post comments by November 1, 2014.


The link to the report is here:


On behalf of the organizing committee, thank you for your assistance!


Organizing Committee


Owen White

Director of Bioinformatics, University of Maryland, Baltimore, School of Medicine

Co-Chair of NIH BD2K  Software Index Workshop


Asif Dhar

Principal & Chief Medical Informatics Officer

Co-Chair of NIH BD2K  Software Index Workshop


Vivien Bonazzi

Senior Advisor for Data Science Technologies (ADDS)

Co-Chair of BD2K Software and Methods Group


Jennifer Couch

Chief, Structural Biology and Molecular Applications Branch

NCI Co-Chair of BD2K Software and Methods Group


Chris Wellington

Program Director (NHGRI)


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PC | 3 Oct 18:13 2014

[Biopython] RMSD and RMS


I am confused, what is the difference between RMSD and RMS?

In protein papers they cite RMSD but biopython returns RMS.

Thank you,

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Asma Riyaz | 2 Oct 20:58 2014

[Biopython] Sigil color SOLID instead of transparent


I am using Genome Diagram to draw features on tracks, and I need to know if there is a way to make the sigil color solid instead of transparent. Since BIGARROW sigil is what I prefer the track line behind each feature is visible.

Since colors for this module are derived from ReportLab, I tried to investigate if there is something that I can use, this is where I reached:

from reportlab.pdfgen.canvas import Canvas
c = Canvas(filename,pagesize=(400,200)) 
c.drawString(25,180, 'solid'

However to use this property 'solid', drawstring needs to be used which is a property of canvas.

What can I do to over ride the default property of transparency for sigil colors? Any Inputs?


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