New BioJava Logo Design Competition

BioJava is organizing a design competition to come up with a new logo.
Anybody can participate:

  • The logo should look modern and be better than the current one (yellow
    circle)

  • The logo should be able to be rendered as a favicon, as well as large
    (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok.

  • Logos shall not look similar in any way to the trademarked Java
    programming language logo. This means no coffee cups in any way.

Deadline:
Deadline for submissions is July 4th.

Announcement of Winner:
The winner of the new logo competition will be announced during BOSC 2016.

Prize:
We will print t-shirts with the new logo and the designer will get a free
t-shirt.

If the designer of the winning new logo will be attending ISMB 2016, the
attending BioJava developers will take the winner out for dinner.

BioJava will carry the new logo on its homepage and GitHub Profile

Details:
For full details of the competition and how to make a submission please
view here:

https://github.com/biojava/logo

Posted in BioJava, Blogroll, BOSC/ISMB, Community, Development, OBF, OBF Projects, Website | Tagged , , , , , , | 2 Comments

Biopython 1.67 released

This was long over-due, but Biopython 1.67 was released earlier today. The most recent delay was due to migrating our website from MediaWiki to GitHub Pages earlier this year, following an OBF server failure.

Source distributions and Windows installers for Biopython 1.66 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but support for Python 2.6 is considered to be deprecated. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Comparison of SeqRecord objects until now has used the default Python object comparison (are they the same instance in memory?). This can be surprising, but comparing all of the attributes would be too complex. As of this release attempting to compare SeqRecord objects should raise an exception instead. If you want the old behaviour, use id(record1) == id(record2) instead.

New experimental module Bio.phenotype is for working with Phenotype Microarray plates in JSON and the machine vendor’s CSV format (contributed by Marco Galardini).

Following the convention used elsewhere in Biopython, there is a new function Bio.KEGG.read(…) for parsing KEGG files expected to contain a single record only – the existing function Bio.KEGG.parse(…) is intended to be used to iterate over multi-record files.

When a gap character is defined, Bio.Seq will now translate gap codons (e.g. “—“) into a single gap (“-“) in the protein sequence. The gap character is inferred from the Seq object’s alphabet, but it can also be passed as an argument to the translate method.

The new NCBI genetic code table 25, covering Candidate Division SR1 and Gracilibacteria, has been added to Bio.Data (and the translation functionality).

The Bio.Entrez interface will automatically use an HTTP POST rather than HTTP GET if the URL would exceed 1000 characters. This is based on NCBI guidelines and the fact that very long queries like complex searches can otherwise trigger an HTTP Error 414 Request URI too long.

Foreign keys are now used when creating BioSQL databases with SQLite3 (this was not possible until SQLite version 3.6.19). The BioSQL taxonomy code now updates the taxon table left/right keys when updating the taxonomy.

There have been some fixes to the MMCIF structure parser which now uses identifiers which better match results from the PDB structure parse.

The restriction enzyme list in Bio.Restriction has been updated to the May 2016 release of REBASE.

The mmCIF parser in Bio.PDB.MMCIFParser has been joined by a second version which only looks at the ATOM and HETATM lines and can be much faster.

The Bio.KEGG.REST will now return unicode text-based handles, except for images which remain as binary bytes-based handles, making it easier to use with the mostly text-based parsers in Biopython.

Note that the BioSQL test configuration information is now in a new file Tests/biosql.ini rather than directly in Tests/test_BioSQL_*.py as before. You can make a copy of the provided example file Tests/biosql.ini.sample as Tests/biosql.ini and edit this if you wish to run the BioSQL tests.

Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 standard coding style, and in converting our docstring documentation to use the reStructuredText markup style.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

  • Aaron Rosenfeld (first contribution)
  • Anders Pitman (first contribution)
  • Barbara Mühlemann (first contribution)
  • Ben Fulton
  • Ben Woodcroft (first contribution)
  • Brandon Invergo
  • Brian Osborne (first contribution)
  • Carlos Pena
  • Chaitanya Gupta (first contribution)
  • Chris Warth (first contribution)
  • Christiam Camacho (first contribution)
  • Connor T. Skennerton
  • David Koppstein (first contribution)
  • Eric Talevich
  • Jacek Śmietański (first contribution)
  • João D Ferreira (first contribution)
  • João Rodrigues
  • Joe Cora (first contribution)
  • Kai Blin
  • Leighton Pritchard
  • Lenna Peterson
  • Marco Galardini (first contribution)
  • Markus Piotrowski
  • Matt Ruffalo (first contribution)
  • Matteo Sticco (first contribution)
  • Nader Morshed (first contribution)
  • Owen Solberg (first contribution)
  • Peter Cock
  • Steve Bond (first contribution)
  • Terry Jones (first contribution)
  • Vincent Davis
  • Zheng Ruan

Again this list of contributors is longer than usual, which is good, but partly reflects the delay since our last release. My apologies.

Posted in Biopython, Blogroll, Code, Development, OBF, OBF Projects | Tagged , , , , | 39 Comments

BOSC 2016 Panel: Growing and Sustaining Open Source Communities

Every year, BOSC includes a panel discussion that offers attendees the chance to engage in conversation with the panelists and each other. BOSC is all about community, so this year’s panel topic–Growing and Sustaining Open Source Communities–is right at the heart of what we do. Since the first BOSC in 2000, we have focused on bringing together open source bioinformatics developers and users to form and expand collaborations and grow the communities that use and improve their tools and resources.

Community projects have resulted in some of the most popular bioinformatics resources. However, there are many challenges that may be encountered as a community effort develops and evolves. For example:

  • How can an open source community integrate a diverse set of participants, including people with different levels of experience, different interests, and different demographic characteristics?
  • How can non-developers (for example, people who primarily write documentation, or who are users of the software) contribute to these projects?
  • What funding approaches have successfully sustained open source communities after any core funding has run out?
  • What technologies have helped open source communities coordinate efficient communication and planning across multiple locations?
  • What organizational models have some of these communities followed?

This panel brings together six people (five panelists plus a moderator) who have worked to sustain open source communities. They will join audience members in an open dialog about challenges encountered during the life cycle of these communities and approaches to addressing them.

Panel chair Mónica Muñoz-Torres is the biocuration lead for Berkeley Bioinformatics Open-Source Projects (BBOP) at Lawrence Berkeley National Laboratory.

Abigail Cabunoc Mayes is the Lead Developer of the Mozilla Science Lab.

Bastian Greshake co-founded openSNP, a crowdsourced/citizen science open data project.

Jamie Whitacre is the technical project manager for Project Jupyter, which grew out of the widely used IPython Notebook.

John Chilton of Penn State is a software developer on the Galaxy project, and one of the co-founders of the Common Workflow Language.

Natasha Wood of the University of Cape Town is the co-founder of the Cape Unseminars in Bioinformatics.

Please see https://www.open-bio.org/wiki/BOSC_2016_Panel for more information about the panelists.

Posted in BOSC/ISMB, Community | 16 Comments

First three OBF travel fellowships awarded

The first round of the Open Bioinformatics Foundation travel fellowship program has granted funds to three open source bioinformatics software developers to help them attend the Bioinformatics Open Source Conference (BOSC) 2016 in Orlando, Florida, this July. The travel fellowship program (announced 1 May 2016) aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Applications for the first round in 2016 were due on April 15, with two more due dates this year on August 15 and December 15.

Out of more than a dozen applicants from four different continents, the OBF Board chose the following three recipients:

  • Dimitra Sarantopoulou of the University of Pennsylvania is an open source bioinformatics developer who focuses on web applications for proteomic analysis.
  • Michael R. Crusoe (@biocrusoe) is the Co-founder & Community Engineer for the Common Workflow Language (CWL), and previously was the lead developer of khmer.
  • Anurag Priyam is a self-taught bioinformaticst who has created several successful open source tools, including  SequenceServer and oswitch, a Docker-based virtual environment switcher.

The OBF Board congratulates the three winners!

This first round has also shown several points of improvement, both for the program description and the application form. We are in the process of making small adjustments to both, and expect to reopen the application form for the next round of funding at the latest by the time BOSC 2016 rolls around (July 8). We encourage others for whom travel costs are a barrier to participating in open source bioinformatics events to apply for this next round (due date is August 15, 2016).

Posted in Blogroll, BOSC/ISMB, Community, OBF, Website | Tagged , , , , , | 5 Comments

Welcome to our Google Summer of Code 2016 students

The Open Bioinformatics Foundation is participating in the Google Summer of Code 2016 program, and last Friday the selected students were announced. Congratulations to all of you, and welcome. I also want to use this opportunity to thank all students who applied. Resources are limited and your proposals did not make it easy to select our finalists. We wish you all the best for your future endeavours, and hope to be able to work with you in future. The field of bioinformatics is a small one after all.

The Open Bioinformatics Foundation gets to host eight student projects this year:

  • Alisha Mechtley will work with the ETE toolkit on tree searching using regular-expression-like queries.
  • Anton Khodak will work on the Common Workflow Language, creating an automated tool wrapper/converter for CWL
  • Christian Fischer will work on the GeneNetwork Genome Browser
  • Graham Dyer will work on openSNP, extending the quantified-self support
  • Julian Mazzitelli will work on a workflow engine for streamed data analysis in Bionode
  • Mariana Nave will improve the prediction for RiPP clusters in antiSMASH
  • Mateus Jabor will work on improving the user experience in openSNP
  • Vivek Rai will work on linking phenotypes to SNPs in openSNP

Please join me in welcoming all of them in the Open Bioinformatics Foundation community and the respective subprojects. It looks like this will be a great summer.

Kai Blin

OBF administrator for GSoC 2016

Posted in Blogroll, Community, Development, Google Summer of Code, OBF, OBF Projects | Tagged , , | 26 Comments

Phyloinformatics Summer of Code supports OBF Travel Fellowship Program

The Open Bioinformatics Foundation is pleased to announce a gift of USD 18,125 from the Phyloinformatics Summer of Code toward the OBF travel fellowship program. The program, announced earlier this year on March 1, aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The program includes but is not limited to the annual Bioinformatics Open Source Conference (BOSC), OBF’s flagship event.

The funds for this gift are a legacy of the seven years during which the National Evolutionary Synthesis Center (NESCent) served as a mentoring organization in the Google Summer of Code™. Over the years, NESCent’s program, the Phyloinformatics Summer of Code, supported dozens of students for three-month paid internships developing open source software for evolutionary and biodiversity informatics.  Each year, Google made a small award to Duke University, NESCent’s administrative home, to support the program, and when NESCent ceased operations in 2015, the funds for this gift remained.

Todd Vision, former Associate Director of Informatics at NESCent, says “With this gift, OBF will carry on the legacy of the Phyloinformatics Summer of Code in building a diverse and collaborative open source bioinformatics community.”

OBF has only been able to underwrite the Travel Fellowship program for an initial 3 years, for at most a handful of awards each year. As Hilmar Lapp, President of OBF’s Board, and former Assistant Director of Informatics at NESCent, explains, “This program is a signature part of our commitment to inclusivity and growing our community, and we are keen to make it a sustained effort. This gift is a key step in that direction, and I hope that we can convince other donors to follow.”

The gift is specifically earmarked for awards to increase diversity at bioinformatics community events. “By targeting travel costs, we hope to remove one barrier to participation. Meeting face to face can be a critical step to becoming part of an existing community.”, says Karen Cranston, OBF Board Member, who ran the Phyloinformatics Summer of Code program for several years while at NESCent.

There have been long-standing ties between the Phyloinformatics Summer of Code and OBF. They have shared project ideas and mentors, and some graduates from the summer program have subsequently taken on prominent roles in OBF’s projects and community. A student from the 2011 summer program, Sarah Hird, even served as the Outreach Coordinator for BOSC 2015, the theme of which was Increasing Diversity.

About OBF: The Open Bioinformatics Foundation (OBF) is a nonprofit volunteer run organization founded in 2001 with a mission to promote the practice and philosophy of open-source software development and open science within the biological research community. OBF is incorporated as an affiliate project of Software in the Public Interest, Inc., a 501(c)(3) fiscal sponsorship organization.

About NESCent: The National Evolutionary Synthesis Center (NESCent) was a science center dedicated to cross-disciplinary research in evolution, jointly operated by Duke University, The University of North Carolina at Chapel Hill, and North Carolina State University from 2004-2015, with support largely from the National Science Foundation. In 2015, it transitioned to the Triangle Center for Evolutionary Medicine (TriCEM).

Posted in Community, Google Summer of Code, OBF | Tagged , , | 4 Comments

BOSC CodeFest 2016

The Bioinformatics Open Source Conference (BOSC) is a two day meeting focused on open source bioinformatics. We aim to encourage and support a friendly, open and productive community that helps us work together to answer hard biological questions. We’ll get together this summer, July 8-9, in Orlando, Florida.

Abstracts for BOSC 2016 talks and posters are due this Friday, April 1st. We want to hear about your research and encourage everyone to submit an abstract. We love talks from newcomers to BOSC as well as established projects: no idea is too big or small. We also offer Travel Fellowships for speakers if money would be a barrier to attending.

Prior to BOSC, we organize a free two day collaborative working session called Codefest. We’ll establish friendships and collaborations while helping new members find fun work and extending existing projects. It’s a time to learn, teach, develop and grow. This year we’re kindly hosted by the FamiLAB workspace in Orlando. So in addition to getting to work with fellow OpenBio members, you’ll have the chance to learn about the Orlando maker community.

We hope you’ll join us in Orlando this summer for Codefest and BOSC. Please send in your abstracts before Friday and sign up on the Codefest page.

Posted in Blogroll, BOSC/ISMB, Community, Development, General, OBF, OBF Projects, Website | Tagged , , , , , | 24 Comments

BOSC 2016 Keynote Speakers

We’re delighted to announce the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2016:

Jennifer Gardy

Jennifer Gardy

Dr. Jennifer Gardy is both a scientist and science communicator. She holds a PhD in Bioinformatics, and is an Assistant Professor of Population and Public Health at the University of British Columbia and a Senior Scientist at the British Columbia Centre for Disease Control (BCCDC). At the BCCDC, she pioneered a new way of investigating outbreaks of infectious diseases – “genomic epidemiology”, which uses a pathogen’s genome sequence as a tool for understanding how an infectious disease spreads. Her group was the first to use genome sequencing to reconstruct a large outbreak of tuberculosis, and she is continuing to apply this novel technique to other outbreak scenarios. She is also involved in other genomics-related research, including replacing traditional laboratory microbiology protocols with single genomic analyses. In 2014, she was appointed the Canada Research Chair in Public Health Genomics, and is Senior Editor at the new open data, open access journal Microbial Genomics.

In addition to her career as a research scientist, Dr. Gardy is known for her work in science communication and education, both in print and on TV. She has made regular appearances on CBC’s documentary series The Nature of Things, has hosted CBC’s eight-part science series Project X, and is a regular guest host on Discovery Channel’s Daily Planet science show. She has written and blogged for the Globe and Mail, has written a children’s book – It’s Catching! The Infectious World of Germs and Microbes – and runs a series of workshops on how to communicate science effectively.

Dr. Gardy’s keynote topic is “The open-source outbreak: can data prevent the next pandemic?”

Every century, something comes along that shakes up public health – vaccines, sanitation, antibiotics – and data promises to be the great disrupter of 21st century infectious disease epidemiology. In the last 5-6 years, genomics has dramatically changed how public health agencies diagnose and investigate diseases from food poisoning to tuberculosis, giving us a new tool to understand and control infections. The change is also apparent at a cultural level – genomics and bioinformatics researchers have largely come from an open data, collaborative space and have brought new ways of thinking to public health laboratories, previously secret, closed organizations. In this talk, we’ll explore some of the dramatic changes in public health microbiology that genomics and bioinformatics has facilitated, and look at how future data sharing efforts in areas such as digital disease detection might be the key to preventing future pandemics.

Homepage: Jennifer Gardy, Twitter: @JenniferGardy


Steven Salzberg

Steven Salzberg

Dr. Steven Salzberg is the Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics and the Director of the Center for Computational Biology in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. From 2005-2011, he was the Director of the Center for Bioinformatics and Computational Biology and the Horvitz Professor of Computer Science at the University of Maryland, College Park. From 1997-2005 he was Senior Director of Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland, one of the world’s leading DNA sequencing centers at the time.

Salzberg’s lab currently focuses on next-generation sequence alignment, genome assembly, and microbiome analysis.They have produced several popular systems for alignment of next-generation sequencing reads, including the Bowtie, Tophat, and Cufflinks systems. All of the group’s software is free and open source, and their systems have been downloaded hundreds of thousands of times.

Dr. Salzberg is a Fellow of the American Association for the Advancement of Science (AAAS) and a Fellow of the International Society for Computational Biology (ISCB). He was the 2013 winner of the Benjamin Franklin Award for Open Access in the Life Sciences, in recognition of his many contributions to open access bioinformatics software and his strong advocacy for open access to data, software and publications.

Dr. Salzberg will speak about “Open source, open access, and open data: why science moves faster in an open world”.

The Human Genome Project established a practice of sharing data rapidly, prior to publication, that has since become a model for many projects in genomics. Data sharing has been slow to penetrate other fields because of many factors, some of which I will discuss in this talk. Nevertheless, sharing of methods, data, and results helps science move ahead faster, and openness is essential for the continual process of checking and self-correction that good science requires. I will discuss some of the successes as well as some noteworthy mistakes that have been discovered thanks to open science.

Homepage: Steven Salzberg, Twitter: @StevenSalzberg1


The BOSC 2016 call for abstracts is currently open, and BOSC/ISMB 2016 registration will open next week. We hope to see you in Florida!

Posted in Blogroll, BOSC/ISMB, Community, General, OBF, Website | Tagged , , , | 19 Comments

BOSC 2016 Call for Abstracts

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

[BOSC Logo]

Important Dates:

[ISMB 2016 logo]
  • Call for one-page abstracts opens: March 1, 2016
  • Abstract submission deadline: April 1, 2016extended to Monday 4 April 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.

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.

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

Posted in Blogroll, BOSC/ISMB, Community, Development, OBF | Tagged , , , | 67 Comments

OBF Travel Fellowship Program

We are very pleased to announce our new Open Bioinformatics Foundation (OBF) Travel Fellowship program. The program is designed to enable people, whether long-standing members of our community or newcomers, to participate in eligible events for which costs would otherwise be prohibitive. This includes our annual Bioinformatics Open Source Conference (BOSC).

Although not limited to specific groups of people, the program constitutes another major step for us in our ongoing efforts to increase the diversity in our communities in particular, and in the open source / open science bioinformatics community in general. As explained in the just published BOSC 2015 report, inclusivity was one of the founding principles of the Bio* open-source project communities that came together under the OBF umbrella, and thus also of BOSC, our flagship event. OBF’s bylaws have included a nondiscrimination clause from the outset. OBF’s major member projects have not only always welcomed new participants to their communities, but embraced passing on leadership to people who hadn’t been part of the “inner circle” from the beginning.

However, being on the “inside” can hide the barriers to joining a community as a newcomer. In practice, the demographics of our member community, and therefore also of BOSC, have mirrored the low diversity observed for open-source project communities in general.

We’ve committed ourselves to address this. We simply owe it to our mission, which is predicated on being inclusive. For BOSC 2015 we chose to make increasing diversity the main theme, including the BOSC 2015 panel discussion. When asked for a show of hands of who was there for the first time, nearly half of the attendees’ hands went up! We believe firmly that with enough dedicated and sustained attention, our community can include everyone who shares our mission. We also believe that eventually more diversity at our community events will trickle down to increasing the diversity of participants in our member projects.

To fund the OBF Travel Fellowship program, we have for now committed an annual budget of $5,000 from our existing assets. At this level, we should be able to sustain the program for a minimum of 3 years.  We would like to do more, and to commit to the program for at least 10 years. To help us accomplish that, we are calling on donors and BOSC sponsors. You can earmark your contribution to be used specifically for funding this program – simply email the Board if the donation form does not leave enough space.

Special thanks for bringing this program to life go to Karen Cranston, who joined the OBF Board in spring 2015 and shepherded the effort from inception to launch.

Posted in BOSC/ISMB, Community, OBF | Tagged , , , , | 61 Comments