Goodbye MediaWiki, hello new website!

Above: the old BOSC page. Below: the new one.

If you’ve been around the OBF and BOSC community, you’re probably familiar with our slightly rusty old site, which ran on MediaWiki, the same open source software that runs Wikipedia. While they’re both awesome tools, we decided it was time for a refresh.

Over the last few months, our Outreachy Intern Deepashree Deshmukh designed and implemented the new OBF website (with supervision by OBF Board member Yo Yehudi). The goal was an attractive and easily-updatable site that can function as a community-oriented hub. Did we accomplish that? Your feedback on the new site is welcome!

What’s going to happen to the old OBF and BOSC websites?

The two old sites – the old wiki / main site at http://www.open-bio.org/wiki and the blog at http://news.obf.org – will stick around for a while, but they won’t be updated any more. One of our goals was to make sure not to break any of our old links – some of them have been around for years. You’ll probably notice a banner at the top of the old pages, pointing towards the new site. Longer term, we’re hoping to redirect all our old URLs directly to their equivalents on the new website.

What to do if you spot any bugs or strange things

We’ve spent a lot of time testing, updating content, tweaking things, and squashing bugs – but no site is ever perfect so it’s possible (probable?!) we’ve missed things. If you spot broken links, layout problems, browser compatibility issues, or anything else, please let us know. If you have a GitHub account, you can log an issue directly, or if it’s easier drop by our gitter homepage chat and let us know there. You’re also welcome to pick the issue up if you know how to fix it!

Acknowledgements

As well as the fantastic hands-on work from Deepashree, we’d like to thank Yo Yehudi for her excellent mentorship of our first OBF intern, Nomi Harris for updating the content and reporting bugs, Hilmar Lapp for setting up a staging server and migrating content to the live site, and the rest of the OBF board and BOSC committee for proofreading and bug reports. A lot of people put time and effort info this and we couldn’t have done it without you!  

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

A week of open source adventures in San Diego

This is a guest blog post from Lindsay Rutter, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend a National Center for Biotechnology Information (NCBI) hackathon and the Plant and Animal Genome Conference (PAG). The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes on 15 April 2019. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships.

I would like to thank the Open Bioinformatics Foundation (OBF) for promoting open source bioinformatics. Many people believe that transparency in science and software helps us procure the most we can out of increasingly large biological datasets. Your support allowed me to embark on a week-long “open source adventure” in San Diego, where I participated in a data science hackathon and introduced my new software package at a conference workshop.

I was up early the first morning for the same reason anyone would be when visiting sunny Southern California – to hunt for viruses computationally! It was great to participate in my third National Center for Biotechnology Information (NCBI) hackathon. The three-day event was hosted by the Computational Sciences Research Center at San Diego State University and our mission was to develop virological indices using 141,000 metagenomic datasets from the NCBI Sequence Read Archive (SRA). Improving the usability of the sheer volumes of data publicly available on the NCBI SRA could potentially facilitate important public health analyses. Hackathon participants split into nine working groups to build a scientific pipeline for metadata processing and novel virus discovery in the cloud infrastructure. Data preparation teams filtered assembled contigs, supervised machine learning teams cleaned metadata, and phylogenetic association teams clustered any matches. Contigs that did not map to known viruses were sent to teams that mapped domains and open reading frames with virus gene families. Based on these results, certain contigs were then sent to “viral dark matter” teams that identified novel viral contigs.

Hackers meeting. (Image shared by Joan Martí-Carreras)

Hackers at work (Image shared by Ben Busby)

There is a lot of problem-solving in hackathons. A lot of divergent thinking. Some sinking or swimming. This particular hackathon was even more animated than usual because all forty participants were working toward the same end pipeline and teams needed to pitch new prototypes to other teams each time a problem was encountered. Hackathon participants ranged from unseasoned students to computational virology experts and travelled from around the world. In the “viral dark matter” team that I led, one teammate flew in from Australia and another teammate flew in from Columbia. Many of us have used version control platforms to remotely collaborate with peers when writing code, but collaborating with people from different experience levels and backgrounds all together in the same room is a unique environment that I believe fosters creativity.

Defining virus indices (Image shared by Ben Busby)

In the end, we produced eight free software artifacts, which are available on GitHub. Annotations and associated metadata will also be freely available in a Jupyter notebook-driven API. Many participants believed the event provided evidence that hackathon settings can be effective for demonstration projects indexing large datasets. We celebrated our work each evening by enjoying delicious food at nearby restaurants. Dinner topics ranged from ancient viruses beneath Arctic ice to synthetic viruses to future virus-hunting hackathons. The daily time reserved for casual discussion with other hackers is a great attribute of NCBI hackathons.

Hackers know how to have fun, even when separated from their computers! (Image shared by Ben Busby).

The Plant and Animal Genome Conference (PAG) commenced the day after the hackathon ended. The conference encourages forum on recent developments and future plans for plant and animal genome projects, an internationally important topic. I was invited to give a talk during their annual workshop “Big Data: Manage your data before your data kills you”. Indeed, big datasets can almost feel like numerical avalanches that we should run away from, but the workshop encouraged attendees to transcend such grim thinking and instead was motivated to spark discussions on how we can properly create, interpret, and share such large datasets.

Twitter feeds for the Big Data workshop.

One speaker discussed guidelines on how to effectively manage and document large datasets. Another speaker tackled a modern bioinformatics nightmare: The maize community had strict rules for gene naming that were rigorously followed for decades until about ten years ago when scientists began assigning names to genes that already had names. Now, the same gene could have multiple names across multiple databases. The speaker suggested developing and abiding by nomenclature committees to fight the problem.

Hexagonal representation for the bigPint package.

I presented my open-source software package called bigPint, which provides interactive visualization methods for large datasets. I was excited to demonstrate the visualization toolkit to a room full of biologists because I think it can be useful for people possessing all levels of statistical background. Scientists need to apply normalization techniques and models to analyze their datasets but this can be difficult for people with little statistical knowledge. Visualization is inherently intuitive and can be used in a complementary fashion with models to allow scientists to better understand which analytical approaches may be the most suitable for their data. I think the workshop all together was aimed at democratizing data. Making data more accessible to more people. Making data easier to share.

After the conference, everyone seemed to want to go to “Charlie’s”. I imagined Charlie was a well-liked and kind intellect who was hosting everyone and who I should probably want to meet, but eventually realized it was just a popular restaurant connected to the conference hotel. I am still glad I went. I met up with the NCBI hackathon organizer Ben and a fellow hacker Jan, two-spirited and sharp-witted individuals who have contributed vastly toward open science. I know firsthand that many hackathon organizers are working hard to increase the inclusiveness at their events. If you are interested in open source software development but are worried whether you will “measure up” or “fit in”, keep in mind that many hackathons do not require advanced computer skills and are a great way to network with other enthusiasts while building those very skills in a supportive environment. One of the most valuable parts of this fellowship was the opportunity to reconnect with old and connect with new open science enthusiasts, and I hope the community continues to grow and diversify in the years to come. Thank you again to the OBF for supporting such a meaningful theme.

Posted in Community, Development, OBF, Travel Fellowship | Tagged | Leave a comment

Google Summer of Code 2018 wrap-up

We have recently applied to Google for the OBF to be part of the Google Summer of Code 2019 programme, again with Kai Blin and Michael Crusoe as joint administrators. Last year, OBF GSoC 2018, was another good year with five students successfully completing their projects:

  • Synchon Mandal (mentor Moritz Beber) “Adding methods to cobrapy for improved constraint-based metabolic modelling.” (first blog bost; final report)
  • Sophia Mersmann (mentors Oliver Alka, Julianus Pfeuffer, and Timo Sachsenberg) “Improve Posterior Error Probability Estimation For Peptide Search Engine Results” (blog posts; final report)
  • Edgar Garriga Nogales (mentors Paolo Di Tommaso, Michael R. Crusoe, and Stian Soiland-Reyes) “Implement the support for Research Object specification into Nextflow framework” (repository; homepage; final report).
  • Sarthak Sehgal (mentors Yo Yehudi, Dennis Schwartz, and Rowland Mosbergen) “Frontend Website Student Project for BioJS” (repository; blog posts; final report).
  • Megh Thakkar (mentors Yo Yehudi, Dennis Schwartz, and Rowland Mosbergen) “Backend Website Student Project for BioJS” (repository; blog posts; final report).

In some cases there isn’t a single code repository to link to, rather their work included pull requests to the main project etc.

Thank you to all our volunteer GSoC administrators and mentors – and of course thank you to the students – we hope you’ll continue to work in bioinformatics and/or open source.

Posted in Blogroll, Code, Community, Development, Google Summer of Code, OBF, Uncategorized | Tagged | Leave a comment

Travel award recipients for December 2018

We had a great round of OBF travel fellowship candidates in our last round of applications, and after review we extended offers to three deserving applicants: Malvika Sharan, Lindsay Rutter, and Sarker Kamruzzaman. They’ve all accepted the award, and we’re looking forward to hearing about their experiences!

Congratulations to our December 2018 recipients:

Malvika Sharan will be attending BOSC at ISMB 2019 in Basel this July. Abstract submissions have only just opened, but she intends to submit an abstract expanding on the idea “Inclusiveness in Open Science” that she spoke about last year (slides). She’s been active in the BOSC community for several years, participating in abstract review and BoF organisation, and she plans to continue this for 2019.

Lindsay Rutter attended the Plant and Animal Genome Conference to give an invited workshop talk for the “Big Data: Manage your data before your data kills you” session. Her software “bigPint” allows biologists to visualize genomics data, especially RNA-sequencing data, and was recently submitted and accepted to Bioconductor.

Sarker Kamruzzaman will be attending the 2019 U.S. Semantic Technologies Symposium in March. He’ll be presenting a tutorial “On the Role of Data Semantics for Explainable AI” as well as a poster. The conference is meant to bring together specialists in many different fields, including natural sciences, so they can benefit from emerging semantic web technologies.

Watch this space for blog posts from each of the awardees.

The next deadline for travel awards is April 15, 2019. 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.

Posted in Community, OBF, Travel Fellowship, Uncategorized | Tagged | Leave a comment

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!

Posted in Uncategorized | Leave a comment

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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