Bosc

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.

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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.

Hello from Berlin, where the pre-BOSC informal CodeFest 2013 meeting is already underway. We’re looking forward to seeing even more of you on Friday and Saturday for BOSC 2013.

BOSC 2013 will be the 14th annual Bioinformatics Open Source Conference, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. This year the ISMB/ECCB 2013 is in Berlin, Germany.

Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012), a Special Interest Group (SIG) of ISMB 2012.

Dates: July 13-14, 2012 Location: Long Beach, California Web site: /wiki/BOSC_2012 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:

• April 13, 2012: Deadline for submitting abstracts
• May 7, 2012: Notification of accepted talk abstracts emailed to authors
• July 11-12, 2012: Codefest 2012 programming session
• July 13-14, 2012: BOSC 2012
• July 15-17, 2012: ISMB 2012

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference ( BOSC 2011), an ISMB 2011 Special Interest Group (SIG).

Dates: July 15-16, 2011 Location: Vienna, Austria Web site: /wiki/BOSC_2011 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:

• April 18, 2011: Deadline for submitting abstracts to BOSC 2011
• May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
• July 13-14, 2011: Codefest 2011 programming session
• July 15-16, 2011: BOSC 2011
• July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

On behalf of the BOSC 2010 Organizing Committee, I am pleased to announce that the BOSC 2010 Proceedings has been published today in BMC Bioinformatics.  Special thanks go to the abstract and proceedings reviewers who helped make this possible.