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.

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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).

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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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Biopython 1.72 released

Dear Biopythoneers,

I’m writing this in Portland at the GCC BOSC 2018 conference, where I will present the Biopython Project Update 2018 talk tomorrow. Yesterday during my airport layover in Iceland, I published the Biopython 1.72 release to our website and PyPI:

https://biopython.org/wiki/Download
https://pypi.python.org/pypi/biopython/1.72

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.

Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and SeqIO.write (especially when used in a for loop).

The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use inclusive end co-ordinates to better handle searches at end points. This will require you to rebuild any existing MAF index files.

In this release 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 Entrez module now supports the NCBI API key. Also you can now set a custom directory for DTD and XSD files. This allows Entrez to be used in environments like AWS Lambda, which restricts write access to specific directories. Improved support for parsing NCBI Entrez XML files that use XSD schemas.

Internal changes to our C code mean that NumPy is no longer required at compile time – only at run time (and only for those modules which use NumPy).

Seq, UnknownSeq, MutableSeq and derived classes now support integer multiplication methods, matching native Python string methods.

A translate method has been added to Bio.SeqFeature that will extract a feature and translate it using the codon_start and transl_table qualifiers of the feature if they are present.

Bio.SearchIO is no longer considered experimental, and so it does not raise warnings anymore when imported.

A new pairwise sequence aligner is available in Bio.Align, as an alternative to the existing pairwise sequence aligner in Bio.pairwise2.

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

  • Benjamin Vaisvil (first contribution)
  • Blaise Li
  • Chad Parmet
  • Chris Rands
  • Connor T. Skennerton
  • Francesco Gastaldello
  • Michiel de Hoon
  • Pamela Russell (first contribution)
  • Peter Cock
  • Spencer Bliven
  • Wibowo ‘Bow’ Arindrarto

Thank you all.

Peter

P.S. You can follow @Biopython on Twitter

Checksums for interest/public record:

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biopython-1.72.zip
$ md5sum biopython-1.72*

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biopython-1.72-cp35-cp35m-manylinux1_x86_64.whl

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biopython-1.72-cp36-cp36m-manylinux1_x86_64.whl

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OBF Birds of a Feather at GCCBOSC 2018

If you’re going to GCCBOSC 2018, we invite you to join us at the OBF Birds of a Feather on Wednesday, June 27, from 5:40-7:40pm. Come and chat over dinner! Everyone is invited, whether you’re a longtime OBF member or someone who’s never even heard of the OBF. (By the way, anyone who is involved in open source or open science is welcome to join the OBF, and there is no membership fee.)
More details at https://gccbosc2018.sched.com/event/FCGp
We look forward to seeing some of you there!

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Travel award recipients for April 2018

We had another great round of applications for the OBF Travel Fellowship this spring. After reviewing the applications, the OBF Board selected three recipients, who have all accepted the award.

Congratulations to our spring 2018 recipients:

Watch this space for blog posts from each of the awardees (update – links added above).

The next deadline for travel awards is August 15. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community.The program is aimed at increasing diverse participation at such events. See the OBF travel award page for details and how to apply.

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Saving science from itself: A review of the 2018 eLife Innovation Sprint

This is a guest blog post from Anisha Keshavan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the 2018 eLife Innovation Sprint in Cambridge, May 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. The current call closes 15 August 2018, you might want to apply?

It is hard for me to put into words the thrill, excitement, and inspiration I’m feeling after attending the 2 day eLife Innovation sprint on May 10th and 11th. The #eLifeSprint (https://elifesciences.org/events/c40798c3/elife-innovation-sprint-2018) in Cambridge, UK, brought together software developers, researchers, designers, and anyone who was passionate about leveraging web technology to advance open scientific communication. The goal: to save science from itself!
Continue reading

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Welcome to our Google Summer of Code 2018 students

The Open Bioinformatics Foundation is again participating in the Google Summer of Code program this year. Last Monday the selected students were announced. Congratulations to all of you, and a heartfelt welcome. I also want to use this opportunity to thank all students who applied. Resources were limited, we did not get all the slots that we asked for, and so we had to make some tough choices.  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, as you will find out.

The Open Bioinformatics Foundation will host six student projects this year:

  • Hitesh Joshi will be working on a Bionode workflow engine for streamed data analysis
  • Synchon Mandal will be improving the constraint-based modeling in COBRApy
  • Sophia Mersmann will improve the posterior error probability estimation for OpenMS peptide search engine results
  • Edgar Garriga Nogales will implement support for Research Object specification into the Nextflow framework
  • Sarthak Sehgal will be rewriting the front-end code powering the BioJS websites
  • Megh Thakkar will be revamping the back-end of the BioJS websites

Please join me in welcoming all of them to the Open  Bioinformatics community and the respective subprojects. I’m sure we’ll have a great, productive summer together.

 

Kai Blin
OBF administrator for GSoC 2018

PS: We ask all our students to blog about their summer of code experience and will be updating this post with links to their respective blogs.

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