Meet our new Travel Fellowship Review Chair: Farah Zaib Khan

Farah presents CWLProv at GCCBOSC 2018

The next round of our OBF Travel Fellowships just ended on the 15th of December! This round we have introduced a Review Chair coming from the midst of our community that will help us in reviewing the applications. The role will be filled by Farah Zaib Khan, one of our OBF Travel Fellowship alumni. Farah has successfully applied for the Fellowship twice before. Thanks in part to this support, she has become a central community member both of the Bioinformatics Open Source Conference and the Open Bioinformatics Foundation itself.

Farah recently completed her PhD at The University of Melbourne, Australia. The OBF travel fellowship helped her interact with the Bioinformatics community during BOSC 2017 and GCCBOSC 2018 where she actively participated in the Codefests and other activities to shape her PhD work. Her PhD research is about the provenance and interoperability of bioinformatics workflows. The funding and support provided by OBF is acknowledged in the article recently submitted by her for publication.

We are happy to see that the Travel Fellowships help students and Early Career Researchers to participate and grow within the Open Bioinformatics community, as well as helping to increase the diversity of participants in Open Bioinformatics events.

Posted in Community, Travel Fellowship | Leave a comment

Biopython 1.73 released

Dear Biopythoneers,

Biopython 1.73 has been released and is available from our website and PyPI.

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement”, or the very similar but more commonly used “3-Clause BSD License”.  See the LICENSE.rst file for more details.

The dictionary-like indexing in Bio.SeqIO and Bio.SearchIO will now explicitly preserve record order to match a behaviour change in the Python standard dict object. This means looping over the index will load the records in the on-disk order, which will be much faster (previously it would be effectively at random, based on the key hash sorting).

The “grant” matrix in Bio.SubsMat.MatrixInfo has been replaced as our original values taken from Gerhard Vogt’s old webpages at EMBL Heidelberg were discovered to be in error. The new values have been transformed following Vogt’s approach, taking the global maximum 215 minus the similarity scores from the original paper Grantham (1974), to give a distance measure.

Double-quote characters in GenBank feature qualifier values in Bio.SeqIO are now escaped as per the NCBI standard. Improperly escaped values trigger a warning on parsing.

There is a new command line wrapper for the BWA-MEM sequence mapper.

The string-based FASTA parsers in Bio.SeqIO.FastaIO have been optimised, which also speeds up parsing FASTA files using Bio.SeqIO.parse().

Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.

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

  • Alona Levy-Jurgenson (first contribution)
  • Ariel Aptekmann
  • Brandon Invergo
  • Catherine Lesuisse
  • Chris Rands
  • Darcy Mason (first contribution)
  • Devang Thakkar (first contribution)
  • Ivan Antonov (first contribution)
  • Jeremy LaBarage (first contribution)
  • Juraj Szász (first contribution)
  • Kai Blin
  • Konstantin Vdovkin (first contribution)
  • Manuel Nuno Melo (first contribution)
  • Maximilian Greil
  • Nick Negretti (first contribution)
  • Peter Cock
  • Rona Costello (first contribution)
  • Spencer Bliven
  • Wibowo ‘Bow’ Arindrarto
  • Yi Hsiao (first contribution)

For reference, checksums:

$ md5sum biopython-1.73*
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$ sha256sum biopython-1.73*
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Posted in Biopython, Blogroll, Code, Community, Development, OBF Projects | Tagged , , , | Leave a comment

Updates are coming!

Brace yourselves - updates are coming

About a year ago, the OBF shared plans to get more involved with the open science community, and followed up by recruiting two board members for this purpose. Since then, we’ve tried to keep up momentum and community engagement – during GCCBOSC, we held an OBF Birds of Feather meeting, allowing members of the board to meet with attendees and discuss their needs and interests. As a result of this meeting, we ended up with our new community-designed logo and launched a community newsletter (incidentally, issue 2 of the newsletter is going to be released within the next few days – feel free to suggest a news item).

OBF + Outreachy Intern = Site Redesign

Our next step is the exciting announcement of a complete site redesign. Over the period of December 2018 – March 2019, Deepashree Deshmukh will be working as an Outreachy Intern, creating a purpose-built CMS powered website for the OBF.  We’d also like to thank all of the other fantastic applicants to this project. Contributors from around the world spent time, effort, and did some genuinely great work prototyping their designs during the application phase.

Currently, the OBF site is comprised of our blog, where you’re probably reading this, a GSoC mini-site, and our main MediaWiki-powered site. We’re looking forward to combining and refreshing these, hopefully resulting in an attractive and easily-updatable site that can function as a community-oriented hub. We’ll be sharing drafts as they evolve. If you have any thoughts or comments on what you’d like to see in the new site, feel free to leave a comment on this post.

 

Posted in Community, Website | Tagged , , , | 2 Comments

OBF membership form fixed

We recently discovered that the application to join the OBF (linked from the OBF membership page) was not working. It broke some time after August 31. We have now replaced it and it is working once again.

If you applied for OBF membership between September 1 and yesterday, please go to the new form (https://goo.gl/x9KYWL) and resubmit your application. We apologize for the inconvenience!

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The color of bioinformatics: what is it and how can it be modified?

This is a guest blog post from Tendai Mutangadura, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the GCCBOSC 2018 meeting in Portland, June 2018. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of three awards from our April 2018 travel fellowships call. Our August call recently closed, the current call closes 15 December 2018, you might want to apply?

When I was selected as one of 3 recipients of the April 2018 OBF Travel Fellowships, I wanted this to signify a turning point in my career. I expected to meet and interact with many great minds in open science and bioinformatics, and the GCC-BOSC 2018 meeting in beautiful Portland exceeded my expectations. Because I was travelling light and had been to Portland once before, I chose to use public transport from PDX to get to Reed College, the meeting venue. This afforded me a mini tour of Portland before getting to the serious but fun business of the meeting. When I stepped off the Reed College bus stop, I flagged down the first person I saw to ask for directions to the registration venue, and this person was none other than Anton, one of the scientists instrumental in the development of the Galaxy project. Great start. As we chatted en route to the registration place, I took the opportunity to brag to him that I had recently figured out the causal mutation associated with a neurodegenerative disease in one of our whole-genome-sequenced dogs using the web-based Galaxy platform.

I attended as many training sessions related to Galaxy on Day 1 of training as I could. I have been a Galaxy platform user for >3 years and had previously attended the GCC 2016, so it was great to meet new and old acquaintances this time round. I even had the opportunity to get help with aspects of my Jetstream account virtual machines during one of the two CollaborationFest days that I attended. I found the CollaborationFest very useful in making new contacts and discussing potential future collaborations.

On Day 2 of Training, the highlights of my training, based my bioinformatics needs, included a 2.5 hour GATK training session and the bcbio workshop. In the latter, Brad Chapman, starring here, talked about and demonstrated how communities can work together to make giant strides in developing robust open source software pipelines and making these freely accessible to anyone, everyone, anywhere. For someone like me, for whom having access to computing resources and setting aside the time to focus on developing or tweaking code as part of my day job can sometimes be an uphill struggle, the bcbio workshop was a godsend. Bcbio allows me to do my day job duties and do bioinformatics too. After the meeting, I immediately contacted one of my XSEDE Extended Collaborative Support Services (ECSS) team members, Phil Blood, to discuss the possibility of putting together a species agnostic variant-calling pipeline. I have already started this project using my XSEDE start-up grant computing resources allocation on Bridges, at the Pittsburgh Supercomputing Center (PSC). So far, I have been off to a good start. For those who may not be aware of the many great free computing resources out there, such resources exist, as I have alluded to above, for anyone to take advantage of.

Now, a light-hearted reference to a serious (according to me), but common observation at conferences such as but definitely not limited to GCC-BOSC: the lack of diversity of attendees. This is what prompted me to title my blog post the way I did. My first answer was (metaphorically speaking) that the color of bioinformatics should be ‘rainbow’. But when I googled ‘rainbow colors’ it occurred to me that the colors black and white are not part of the rainbow. I also refreshed my rusty optical physics and got explanations why this is the case. Now, to get back on track, would it not be wonderful if more people of color were involved in this bioinformatics revolution? What can be done to redress this current state of affairs? Thumbs up to the OBF for recognizing and doing something about this lack of diversity by creating the OBF Travel Fellowship! For my part, when and if I complete any pipeline(s) based on bcbio code, I plan to publish a collection of such pipelines online as self-paced tutorials (the website will go live soon) in a very user-friendly format targeted to those who are command line challenged, from any community, to encourage them to get started in bioinformatics analyses, or at least analyze their own data without buying expensive commercial packages. This would be my way, albeit at very small scale, of democratizing bioinformatics. One of the advantages of involving people with as diverse backgrounds as possible with basic training in bioinformatics and genomics is that this may help reduce mistrusts linked to unfortunate historical incidents such as the Tuskegee experiments, not only for countries like the US but anywhere around the world where similar types of mistrust may exist.

Posted in Blogroll, BOSC/ISMB, Community, OBF, Travel Fellowship, Uncategorized | Tagged , , , , , , | Leave a comment

City of roses they call it – Portland Oregon (USA)

This gallery contains 3 photos.

How should I start describing the fruitful experience in this amazing city… First time ever in Portland, second time attending BOSC… I knew I was signing up for a great time but did not know much about the uncanny beauty … Continue reading

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Taking Turns

BOSC 2019 will be part of ISMB 2019

Every year until 2018, BOSC was part of the annual ISMB conference as a community of special interest (COSI, formerly known as a SIG, Special Interest Group). As part of our continuing quest to broaden and deepen the BOSC community, we decided to perform an experiment this year by partnering with the Galaxy Community Conference rather than with ISMB. As we reported, the experiment was a success–participants were overwhelmingly positive about the experience, and the conference did attract a somewhat different mix of attendees than in past years. However, we also concluded that there are some advantages to meeting with ISMB–for example, it attracts more students and postdocs, and the presence of other COSI tracks provides a wider range of scientific topics. Moreover, unlike the GCC 2018 venue, the venue already chosen for GCC 2019 has a number of drawbacks: we wouldn’t be able to run similarly-sized parallel sessions; registration prices wouldn’t be as affordable as in 2018; and the venue would not be able to accommodate the larger (160 people) and longer (four days) CollaborationFest that was one of the highlights of GCCBOSC 2018.

For these and other reasons, the BOSC organizing committee concluded that the best way to serve the broadest community of potential BOSC attendees will be to partner with ISMB some years and GCC some years. We therefore plan to hold BOSC 2019 in Basel as part of ISMB. We hope to partner with GCC in 2020 at a North American site to be determined, or in 2021 in Europe.

Wherever we hold future BOSCs, you can be sure that they will include a wide range of topics in open science and open source bioinformatics, and we hope that they will draw an ever-diversifying mix of attendees. As always, we welcome your feedback about what you liked in past BOSCs and your suggestions for the future. Feel free to email us (bosc@open-bio.org) or tweet (@OBF_BOSC).

Posted in Blogroll, BOSC/ISMB, Community, OBF, Uncategorized | Tagged , , , , , | Leave a comment

GCCBOSC 2018 post-meeting report

This year, the Galaxy Community Conference (GCC) and the Bioinformatics Community Conference (BOSC) met together to form the first Bioinformatics Community Conference. At GCCBOSC 2018, participants were able to meet and collaborate with a broad community of bioinformatics developers and users who focus on open, interoperable software tools and libraries that facilitate scientific research.

Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC attracted nearly 300 participants from around the world. The meeting started with two days of training workshops (Figure 1). The main meeting had some parallel sessions and some joint sessions, including well-received keynote talks by Tracy Teal, Fernando Pérez and Lucia Peixoto, as well as a panel discussion about documentation and training. Posters, demos and Birds of a Feather sessions (BoFs) gave participants opportunities to engage in discussions about topics of mutual interest. After the main meeting, many attendees stayed for up to four additional collaboration days (the CollaborationFest, or CoFest).


Figure 1. Participants at one of the GCCBOSC training workshops. (All GCCBOSC photographs in this post are from Bérénice Batut’s Flickr album, under a CC-BY-SA license.)


Figures 2,3. Attendees and presenters mingled at the poster/demo sessions.


Figure 4. CoFest attendees assembled for morning meetings before breaking into smaller groups to work on collaborative projects.

There was wide agreement among GCCBOSC participants that the meeting was informative, productive and enjoyable. Comments from participants in the post-meeting survey included, “Loved the mix of communities!”, “Location was great,” and “Nice conference. Nice atmosphere. Nice people. I really enjoyed it. Thanks!”. The training workshops and extended CoFest were mentioned by participants as great features of the meeting. Most of the survey respondents who had previously attended a GCC or BOSC rated this year’s meeting as similar or better than past meetings (Figure 5). The main complaint was that the parallel GCC and BOSC sessions forced attendees to choose between them–an embarrassment of riches.

Figure 5: Responses to post-GCCBOSC survey questions from those who had been to previous GCCs or previous BOSCs.

Although post-meeting feedback was almost entirely positive, we did receive two reports of behavior at GCCBOSC that the reporter perceived as not consistent with the spirit of the Code of Conduct. These were handled by the GCCBOSC organizing committee, and everyone involved is satisfied with the outcome. The discussions held by the organizers around these issues led us to re-examine the CoC and think about how we might want to revise it for future meetings. Your input on this topic (or anything regarding GCCBOSC) is welcome.

We are grateful to all those who helped make GCCBOSC 2018 a success: the organizers, presenters, workshop leaders, participants, and our generous sponsors, including Platinum sponsor Google Cloud and Gold sponsor Lenovo + Intel. Thanks in part to sponsor funding, we were able to offer subsidized child care and an onsite lactation room that enabled a speaker who would otherwise have been unable to attend to bring her four-month-old baby and participate actively in the meeting.

Whether or not you attended GCCBOSC 2018, we look forward to interacting with you in the future!

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Following up from BOSC’s OBF Birds of a Feather meeting

It was really great to meet so many of you at GCCBOSC this year! We will soon have a couple of Travel Fellowship blog posts talking about the conference, so we won’t provide too much of a general overview at this point, but we would like to share a little more about one of the Bird of Feather (BoF) events we ran – specifically the OBF community BoF.

The aim of this BoF was to engage anyone who was:

  • Curious about the OBF
  • Interested in suggesting ideas
  • Wanting to help or get more involved with the OBF

The OBF BoF started with a pre-dinner round where we all introduced ourselves and why we were interested in the OBF, and a second round after a quick bite and relocating inside – Portland can get chilly fast in the evening!

Motivations for participating in the BoF included a desire to help people who come from a software background learn more about the biology / bioinformatics side of things. Other participants shared the feeling that they loved the conference but weren’t sure how to take home the “open / good practices make for better software and better research” message we were trying to share.

We ended up with lot of brainstorming and helpful discussions – here are some of the topics.

OBF logo and site

The OBF logo is over a decade old now and looks a little… dated. When we floated the idea of redesigning it at the meeting, we didn’t expect to have sketches roughed out by several attendees before the end of the BoF meeting! We’ve ended up with three different design sets, which you can check out or comment on in this GitHub issue. We’re also considering updating the entire OBF site, if we can find someone to work on that (possibly a summer intern).

Increasing year-round sense of community

For many people, BOSC and the OBF are approximately the same thing – which makes sense, since BOSC is one of the biggest and most noticable things we do. We’d like to support open bioinformatics all year, though. Possible ways we could do this:

  • Local OBF / bioinformatics meetups or hackathons. If the OBF created guidelines for this, would you be interested in running a group in your area?
  • Newsletters with project updates, interesting open / bioinformatics news, events, etc.
  • “How to be open in bioinformatics” webinar – a sort of “open 101” for projects that are interested in being open but aren’t sure where to start. This would be a nice way to kick-start projects that want to present a poster or talk at BOSC but don’t yet meet the openness requirements. (Note that anyone is allowed to attend BOSC, whether or not they have any open repositories – it’s only presenting that mandates a fully open project.)

Joining the OBF as a project or individual

A pertinent question asked at the BoF was: why join, as an individual? Many people have attended BOSC multiple times and even been heavily involved in the community without officially being in the rolls of registered members. The primary reason to join is the ability for membership to vote on issues pertaining to the OBF. In the next few months, we’re hoping to run a vote on changing OBF bylaws pertaining to how projects join, as well as a plain to adopt a Code of Conduct that may apply to both the OBF and its member projects. If this matters to you because A) you care about a project that might be joining soon (there are a couple!) or B) you’d like to see the OBF adopt a more explicit behaviour standard in the form of a CoC, please join the OBF so you can vote!

Get involved

After reading all this, if you’re interested in helping out with any of the ideas or initiatives suggested, please follow up by any of these mechanisms:

  • Open an issue on our OBF-docs repo – this is our preferred method as it allows others to chime in easily and is less transient than a tweet.
  • Leaving a comment on this post!
  • Tweet to @obf_news

Also – please don’t forget to join the OBF if you haven’t already. Any BOSC attendee automatically qualifies for membership, and even if you haven’t attended BOSC before, if you’re reading this post there’s a good chance you’ll fulfil the requirements anyway. Details are in the form!

 

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