Information & Computational Sciences

Mozilla Science Fellowship Application 2016

By on 30/01/2017 in ICS

Last summer I applied to the  Mozilla Fellows for Science 2016 call. Congratulations to the four 2016 fellows, selected from an impressive 483 submissions for only the second year of this innovative program.

I was delighted to be short listed and interviewed, but also slightly relieved not to have made the final cut. This is due to the timing of personal circumstances – I’m now a father, and despite the taking time off under the UK’s Shared Parental Leave scheme, I’m currently trying to cut back work related activities.

While preparing my application, I was impressed by Jon Tennant’s decision to post his application openly online, and had been meaning to share mine too. Better late than never?

[Update: To be clear, this was my application in 2016, which was shortlisted but ultimately unsuccessful]
What follows were my answers to the non-administrative questions on the application web form (including the original typos, plus some minor notes in italics), and my cover letter text.

In addition, I had to provide a CV, and letter of support from my line manager, Leighton Pritchard. I am incredibly grateful – his support letter was glowing, and I felt he did a better job promoting me for the fellowship than my own dry style. Our head of department Rupert Hough also encouraged me, and HR helped to work out a way the fellowship funding could be handled. I would also like to thank Richard Smith-Unna, one of the inaugural Mozilla Fellows for Science 2015, for taking the time to discuss the scheme, and his encouragement.

What institution are you based at currently? (10 words)

The James Hutton Institute, Dundee, Scotland, UK

What is your role at the institution?

Research staff (picked from a drop down list)

What research fields are you in? (25 words)

Bioinformatics, particularly analysis of DNA and RNA sequence data for genome level analysis of plant pathogens in the context of improving and sustaining agricultural yields.

What is your research focus? (50 words)

The applied focus has been on the genomic analysis of plant pathogens, particularly nematode worms and plant viruses, using DNA and RNA sequencing. To support this much of my work is on infrastructure maintaining an internal Galaxy server for my colleagues to run bioinformatics tools and workflows within a web-browser.

Describe to us your current research team. (50 words)

The institute operates a project-centric management system where staff members can be part of multiple projects. This is particularly true for bioinformaticians like myself, as I am and have been involved in multiple projects with different teams. Currently my main focus is plant pathogenic nematodes with mainly wet-lab biologists.

Describe to us how open science advances your research. (100 words)

Historically following the precedent of early major efforts like the Human Genome project, genomic data including raw DNA and RNA sequencing data is generally openly shared in public repositories upon publication. However, we still struggle with groups hoarding genomic resources prior to publication, which has hampered genomic comparison work.

On the software side, we are fortunate that open source is the dominant model for bioinformatics tool and algorithm development, allowing free sharing of ideas and methods. From a practical perspective this allows packaging for automated installation and wrapping tools for use in other contexts like browser-based front ends.

Are you leading any projects related to open science? (100 words)

I co-chair the Bioinformatics Open Source Conference (BOSC) – an annual meeting with around 100 attendees. Much of the work presented is also explicitly about open science, and related themes like data sharing and integration.

[I have now stepped down as co-chair for BOSC 2017, but remain part of the organising committee.]

Since 2009 I have been de-facto project lead for Biopython, an open source Python library for computational molecular biology developed by an international volunteer based team since 1999. See http://biopython.org http://dx.doi.org/10.1093/bioinformatics/btp163

I started and maintain several bioinformatics tool wrappers for the Galaxy web-based platform, including the widely used NCBI BLAST+ tools (see https://github.com/peterjc/galaxy_blast and http://dx.doi.org/10.1186/s13742-015-0080-7 ), and sequence analysis tools (see https://github.com/peterjc/pico_galaxy and http://dx.doi.org/10.7717/peerj.167 ).

How do you see Mozilla advancing your work? (50 words)

This fellowship would allow me to focus on open source development and community work which does not fit neatly into my current job, such as organising the Bioinformatics Open Source Conference (BOSC), secretary to the Open Bioinformatics Foundation (OBF), completing and using my Software Carpentry trainer qualification.

[When my term as OBF secretary expired, I took on the role of treasurer instead.]

What do you see as the opportunities for impact around open research at your university? Could you leverage this opportunity in a potential project? (50 words)

I write a technical blog at http://blastedbio.blogspot.com and would like the group to do do something similar to highlight our work.

The institute already releases a lot of open source software including https://ics.hutton.ac.uk/software/ and I would like to promote further use of GitHub at https://github.com/HuttonICS to encourage external contributions.

What do you think needs to change most immediately in scientific research? (100 words)

Complete adoption of open-access for scientific publications, making them both free-of-cost to read (e.g. to the public who as tax payers may have funded the work) and also re-use (e.g. large scale data-mining).

I believe this best route to achieve this is funding mandates, backed by financial penalties for non-compliance.

I accept that in the short term a 6 or 12 month paid-access embargo period might be a useful compromise.

The recent EU decision to require Open Access for work funded in Horizon 2020 is a very positive step in this directly [sic, should have been direction], but all funders need to encourage this.

What project in the field do you find most inspiring to further science and the web? (50 words)

Although slightly outside my area, http://www.alltrials.net (campaigning to register all medical trials) and the closely related http://compare-trials.org/ (tracking switched outcomes in clinical trials) projects are a combination of web-based public engagement, evidence driven medicine, scientific rigour, and open data sharing – born out of Ben Goldacre blogging as a young doctor.

Why is the the open web important to you? (25 words)

Openness allows data sharing and innovative data integration. Also open web technologies are one of few roots [sic, should have been routes] for today’s children to understand how computers work.

GitHub or other code repository profile

https://github.com/peterjc

Links to 2 of your projects that have high relevance to open science

https://github.com/biopython/biopython

https://www.open-bio.org/wiki/BOSC

Are you comfortable with semi-regular travel, and what are your travel constraints?

Comfortable with regular travel (and have lived in multiple countries), but shorter trips preferred as we’re expecting our first child [rest of answer redacted].

Cover Letter

15 July 2016

To the Mozilla Science Fellowship Selection Committee,

I am writing to apply for the Mozilla Fellowships for Science.

I have been aware of the Mozilla Project for a long time – I used Netscape as my main internet browser as an undergraduate, and was an early adopter of Pheonix (and later Firefox). Mozilla has undoubtedly changed the internet by promoting competition, innovations and standards, and I am excited to see what changes Mozilla Science Foundation can spur in how science works. I hope to contribute to this work.

I am a bioinformatician, a computational biologist working mainly with genome data of plant pathogens. We are fortunate that there is a strong tradition of sharing genomic data, and releasing bioinformatics software as open source – but this is by no means universal, and continued advocacy is needed to improve openness and reproducibility in science.

The Mozilla Fellowship would allow me to focus on and expand my efforts on the open source and related outreach activities. I would continue to serve on the Open Bioinformatics Foundation (OBF) board of directors, again help organize our annual Bioinformatics Open Source Conference (BOSC), and devote more time to the Biopython codebase and community. For example, I would like to mentor another Google Summer of Code student. Taking advantage of the potential travel support, I would want to be more active within the Software Carpentry community, and also attend (or organize) developer gathering like the Debian Packaging Sprints.

As a relatively young field, like many bioinformaticians my career path has not followed the traditional university academic route. I first studied Mathematics and Physics, and then worked for several years as a systems analysist/programmer at a small company doing software integration and modification. Here I learnt important skills like software testing, using shared version control systems, and learnt first-hand the value of properly documented data standards, and the handicap of working with closed-source tools. With hindsight after returning to academia, this experience was important in helping me see the advantages of, and actively embracing, open source for scientific programming.

After this spell in industry, I returned to university to complete an interdisciplinary MSc and PhD. My project was a mixture of wet-lab experiments and computational sequence analysis, which led me to start using, and then contributing to, the open source Biopython project.

At the end of my PhD I joined the Scottish Crop Research Institute, which is now post-merger The James Hutton Institute. I am grateful that the Institute, and in particular my line manager Dr. Leighton Pritchard, have recognized and supported my continued open source, open standards, and open science work.

However, as institute funding has grown tighter with a growing emphasis on securing external project funding, securing travel funding and dedicating work time to these activities has been getting harder. I recognize that with imminent fatherhood, despite my passion, as things stand I will soon have to scale back my unpaid community work after hours.

Reducing my hours at the Institute to 20% during the fellowship, as proposed by our human resources department, will be enough to sustain my key institute commitments – including co- supervision of PhD students. I have already been pushing for more openness within the institute, in particular within our Information and Computational Sciences Group, and the fellowship would allow me to spend more time on this. Specific goals include establishing a developer-slated shared group blog, and having recently secured agreement to create a shared GitHub account, I want to expand uptake of this – especially amongst my colleagues already releasing open source scientific software.

This arrangement would let me spend 80% of my working week as a Mozilla Fellow within our institute, actively engaged with the international open scientific community beyond what I have achieved to-date.

Thank you for taking the time to evaluate this application, and for establishing this unique fellowship scheme.

Sincerely,

Dr Peter Cock
Research Scientist

 

Note: This post was first published on my personal blog, Blasted Bioinformatics: https://blastedbio.blogspot.co.uk/2017/01/mozilla-science-fellowship-application.html

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