Announcing the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2015:

Holly Bik

Dr Holly Bik is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. She obtained her Ph.D. in molecular phylogenetics at the University of Southampton, UK (working in conjunction with the Natural History Museum, London), followed by subsequent postdoctoral appointments at the Hubbard Center for Genome Studies at the University of New Hampshire and the UC Davis Genome Center.

Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015), a Special Interest Group (SIG) of ISMB/ECCB 2015.

• Dates: 10-11 July, 2015
• Location: Dublin, Ireland
• Web site: /wiki/BOSC_2015
• Email: bosc@open-bio.org
• BOSC announcements mailing list
• Twitter: @OBF_BOSC and @OBF_News

Important Dates:

• March 24, 2015: Registration opens for ISMB and BOSC ( https://www.iscb.org/ismbeccb2015-registration)
• April 3, 2015: Deadline for submitting BOSC abstracts
• May 3, 2015: Notification of accepted talk abstracts emailed to authors
• July 8-9, 2015: BOSC Codefest 2015, Dublin
• July 10-11, 2015: BOSC 2015, Dublin
• July 10-14, 2015: ISMB/ECCB 2015, Dublin

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. We particularly wish to invite those who have not participated in previous BOSCs to join us this year!

The BOSC 2015 Organizing Committee is pleased to welcome Sarah Hird as our new Outreach Coordinator. BOSC is eager to increase the participation of individuals and groups that have been historically underrepresented at our conferences, and Sarah will be spearheading this effort.

Sarah is currently a UC Davis Chancellor’s Postdoctoral Fellow with Jonathan Eisen in the UC Davis Genome Center, where her research interests lie at the intersection of phylogeography, bioinformatics and microbial diversity.  She earned her PhD in biology and bioinformatics at LSU. Sarah is also known for her focus on promoting diversity in STEM. “I am personally and professionally interested in how we can make “the Academy” a more representative sample of the world around us,” she says.

We have asked you, and you have spoken! 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they’d like to see, and — most importantly — what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) rather than as an ISMB/ECCB SIG in Dublin (Ireland)..

Under this plan, BOSC 2015 would have been shortly before ISMB/ECCB, but in Norwich. We would have been hosted by The Genome Analysis Centre (TGAC) just after and co-located with the Galaxy Community Conference 2015 (GCC 2015, hosted by The Sainsbury Laboratory). Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority preferred BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin right before ISMB/ECCB 2015.

Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!

The OBF will be holding the fifth annual BOSC Codefest, an informal two day “hackathon” or “coding festival” preceding the Bioinformatics Open Source Conference (BOSC 2014) in Boston (USA).

This year, the BOSC Codefest 2014 is being hosted by hack/reduce (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by Curoverse (the team behind the open source platform Arvados) and Harbinger Partners, Inc. Thanks to this sponsorship, this year the organisers will able to include catering for the participants - I’m expecting at least coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and Jolt Cola doesn’t exist in the USA any more… so I’m waiting to see what our local organisers Brad Chapman & Michael Heuer have planned.

To encourage more student presentations at the Bioinformatics Open Source Conference (BOSC), this year we’re waiving the registration fee for accepted student presenters. When you submit your abstract ( BOSC abstract call open until 4th April), you must tick the student box:

Student submissions must have a full-time student as the first named and presenting author, and be mostly written by students.

Please note that because BOSC registration is via the ISCB as one of the ISCM SIG meetings, eligible students must contact us before filling in their ISCB registration to ensure the BOSC SIG fee is waived.

Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014), a Special Interest Group (SIG) of ISMB 2014.

• Dates: July 11-12, 2014
• Location: Boston, MA, USA
• Web site: /wiki/BOSC_2014
• Email: bosc@open-bio.org
• BOSC announcements mailing list
• Twitter: @OBF_BOSC and @OBF_News

Important Dates:

• March 24, 2014: Registration opens for ISMB and BOSC
• April 4, 2014: Deadline for submitting BOSC abstracts
• May 1, 204: Notification of accepted talk abstracts emailed to authors
• July 9-10, 2014: BOSC Codefest 2014, Boston
• July 11-12, 2014: BOSC 2014, Boston
• July 11-15, 2014: ISMB 2014, Boston

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.

Thanks to those who participated in the BOSC 2014 Keynote Competition! Our winner is Manuel Corpas, who correctly surmised Philip Bourne:

https://twitter.com/manuelcorpas/status/412520369044463616

(In fact, we had already confirmed Philip Bourne as our second keynote speaker before his new job at NIH was announced.) Congratulations, Manuel, on winning free admission to BOSC 2014!

Dr. Bourne’s keynote talk will be entitled “Biomedical Research as an Open Digital Enterprise”:

The biomedical research lifecycle is fast becoming completely digital and increasingly open to the point that publishing could simply become changing the access control on given research objects comprising ideas, hypotheses, data, software, results, conclusions, reviews, grants and so on. This offers immense opportunities for software developers to enable the enterprise. I will describe a vision for the digital enterprise and what the NIH and others are doing to support the notion with the intent to accelerate scientific discovery.

[Read More]

We’re pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference ( BOSC 2014) will be C. Titus Brown, as he announced on Twitter recently:

Titus Brown (@ctitusbrown):
Excited to be a keynote speaker at BOSC 2014! My title: “A History of Bioinformatics (in the year 2039)” - plenty of room for mischief ;)
https://twitter.com/ctitusbrown/status/410934403565490176

In recognition of the growing use of Twitter and social media within science as a way of connecting across geographical divides, we’re announcing a Twitter competition to guess who is scheduled to give the second keynote at BOSC 2014 in Boston.

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI).

Python support

This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported.

We still fully support Python 2.5, 2.6, and 2.7. Support under Jython is available for versions 2.5 and 2.7 and under PyPy for versions 1.9 and 2.0. However, unlike CPython, Jython and PyPy support is partial: NumPy and our C extensions are not covered.