Arabidopsis Information Portal at PAGXXIII

Last Monday the Arabidopsis community gathered for the Arabidopsis Information Portal workshop at PAG XXIII. The Arabidopsis Informatics Portal (AIP) was funded by NSF and BBSRC to move beyond the Arabidopsis genome resource provided by TAIR toward linking the genome to the epigenome, proteome, transcriptome and interactome.

AraportThe first talk was a short update from Eva Huala, formerly of TAIR and now of Phoenix Bioinformatics, the nonprofit company she started in order to keep TAIR going. Huala explained that after TAIR’s NSF funding ended, the pay-to-access model was chosen over the alternative pay-to-submit (open access) approach. This means TAIR is focussed on ensuring the subscribers get the best possible value for money by providing the best possible database curation, manual annotation and user experience. Most TAIR subscription fees are paid by libraries, as if it was a journal, but researchers from institutions whose libraries do not pay the fee will be able to access TAIR’s manual annotation after a year’s embargo.

Next, Sean May (NASC, University of Nottingham) explained that NASC is a module of AIP and is currently integrating with the ABRC. He is consulting the community about the development of NASC, so make sure you have your say in the NASC Strategy Survey:

Chia-yi Cheng (JCVI) gave an overview of Araport, the online home of the AIP. Araport federates diverse datasets from other places, for example TAIR, UniProt and BAR, and maintains the Col-0 ‘gold standard’ annotation. It uses JBrowse as the default genome browser and hosts datasets including the CoGe epigenomics resource, which I blogged about last week. (more…)

Guest post: Software Carpentry for Plant Scientists bootcamp

Categories: guest blogger, Workshops
Comments: No Comments
Published on: December 2, 2014
Software Carpentry Liverpool
Photos from the Bootcamp. Instructors and helpers shown in the bottom photo: Bert Overduin, Marios Isaakidis, Kwasi Kwakwa, Fatima Silva.

Thanks to Robyn Drinkwater from the Royal Botanic Garden Edinburgh for this guest post about the Software Carpentry Bootcamp we ran with CGR Liverpool a couple of weeks ago. This piece was first published on Botanics Stories, the RBGE blog. 

Programming is becoming an increasingly useful skill as it can aid in the execution of large, repetitive tasks, and in running analyses of large data sets. Four staff from RBGE recently attended a workshop set up by GARNet and the University of Liverpool’s Centre for Genomic Research along with Software Carpentry, to help them learn and improve their use of some simple tools and programming.

During the workshop they explored the principles of good programming, which can be applied to any programming language, the use of the Command Line, version control using Git and GitHub, and Python, a widely used programming language, which can be used for data manipulation, as well as other programming tasks.

The workshop led us from first principles through each tool, building our understanding of how it works, and showing us examples of how it could be used. During the workshop we started to explore how we could use these tools to look at our own data, and for some of us, we were still seeing what we could do on the train home!

The next step for all of us is to keep practicing and looking at how we can use Python, Git and the Command Line in our work and keep building on the good foundation the bootcamp gave us.

Tweets from participants and organisers of the event have all been brought together by the organisers:

Image credit: Charis Cook

Software Carpentry Bootcamp: An organiser’s story

Categories: resource, Workshops
Comments: 1 Comment
Published on: November 27, 2014

Lisa and I have been involved in two Software Carpentry Bootcamps this year: firstly the hosts of a Bootcamp in April at the University of Warwick, and the second, just last week, at a Bootcamp co-organised with the Centre for Genomic Research at the University of Liverpool. A few people at the Liverpool event expressed interest in organising their own workshops, so we thought we would talk you through the stages of hosting a bootcamp and share our experiences to help you decide whether you want to run one of your own.


1. Early planning: Decide where the event will be, who will pay, who your audience is and what topics you want to be covered.

It is (now) not free to host a Software Carpentry event. When we organised the Warwick Bootcamp, Software Carpentry was subsidised by the Mozilla Foundation, but since the recent move to its own Software Carpentry Foundation, events now command a fee (TBC) – it’s still a non-profit organisation though.

Software Carpentry trainers are volunteers but you will need to be able to reimburse their travel, food and accommodation expenses. They can come from anywhere in the world, so budget for transatlantic flights!

Other costs you will need to think about include venue hire, and travel, food and accommodation for the workshop participants. It is also up to you whether you want to charge people to attend the workshop to recoup some or all of your costs. For our first bootcamp at Warwick we had sufficient funding to make the event free for attendees, and we paid for one nights’ accommodation too. Because it was free, we did get some last-minute drop-outs, but we had a long waiting list to fill the empty spaces. At the Liverpool event, trainees paid a small registration fee, and paid for their accommodation themselves. Both events booked up quickly and were oversubscribed, so either model works.

We provided lunch and refreshments during both workshops (caffeine breaks are definitely recommended!), and also organised a dinner on the first night of the workshop.

Both of our bootcamps were for complete beginners, but if there are specific topics you need to cover, Software Carpentry can tailor a programme to your needs.


2. First contact with Software Carpentry: If you’re in the UK, the Software Sustainability Institute (SSI) in Edinburgh is your point of contact for organising Software Carpentry events. There is information and an email address on the Software Carpentry website.

Discuss your ideas for the bootcamp with Software Carpentry. We worked with Aleksandra Pawlik and Giacamo Peru from SSI over Skype and via email. Software Carpentry requires core topics to be covered, so there may be some negotiating as you work it out. As our bootcamps were for absolute beginners, unlike most Software Carpentry events, this took some time but was not at all difficult to sort out.

Decide on a date, making sure to consider other events that might limit both trainees and instructors.

The Software Carpentry website suggests being flexible with the dates to make finding instructors easier. I think this would mean pulling a bootcamp together very quickly, which might be ok for an institutional event but was impossible for us.


GARNet and CGR Liverpool present Software Carpentry

Categories: GARNet, Workshops
Comments: No Comments
Published on: September 9, 2014

SWC Liverpool v1


On 17th-18th November 2014, GARNet and the University of Liverpool’s Centre for Genomic Research are teaming up with Software Carpentry in Liverpool for the second Software Carpentry for Plant Scientists bootcamp.

Software Carpentry teaches principles of good programming applicable to any coding language or application, whether sequencing data, phenotypic trait analysis or biochemical assays. Tutorials will start from first principles and cover using Command Line, Python programming including data manipulation with Python, and version control using Git and GitHub. Teaching will be a combination of live coding guided by the trainer and independent practical exercises.

Although the content is suitable for complete beginners, researchers with some experience of programming will also benefit from being taught good practice like version control and test-driven development. These practices will make your programs more sustainable, vastly reducing replication in your code over time, and make them easier to share with team members, collaborators and even in publications.

The programme and tutorials from the first Software Carpentry for Plant Scientists bootcamp is here. This information is to give potential delegates an idea of what the Liverpool event will be like – please be aware that the upcoming bootcamp event will be run by different trainers and therefore will not be exactly the same as the previous one.

To apply for a place on the bootcamp, email between 9th and 23rd September 2014. In your email, please include:

  • Your name
  • Whether you are a student, post-doc, PI or hold another position
  • A brief description of your research interests (less than 50 words)
  • Why you would like to attend the bootcamp (less than 50 words)

Successful applicants will then be invited to register for the workshop from 29th September.

In pictures: Software Carpentry for Plant Scientists

Comments: 1 Comment
Published on: April 11, 2014

Over 30 plant scientists gathered at the University of Warwick this week for our Software Carpentry for Plant Scientists bootcamp. Together we learned to move through space and time using Git, how to make, explore and delete files and directories, how to use Version Control and how to program defensively. As ever we encouraged everyone to Tweet about the event and we’ve collected the tweets in a Storify, which you can access here:

Some photos from the event are below – enjoy! The photo on the second row is the team that made the event such a success. From left to right: Jason Piper, Charis Cook, Leonor Garcia Gutierrez, Aleksandra Pawlik, Christina Koch and Lisa Martin. Thanks especially to our trainers Aleksandra (sent to us from the Software Sustainability Institute, UK) and Christina, who came all the way from Vancouver.


Opportunities in plant science, via social media

Categories: Arabidopsis, Workshops
Comments: No Comments
Published on: March 5, 2014

I don’t usually put this kind of thing on the blog – it’s prime mailing list fodder. But I was writing a round-up post and this section got more than long enough for its own post!

If you’re on our ArabUK mailing list, you’ve probably noticed a flurry of activity this week. There are a lot of post-doc and other job opportunities out there at the moment – Oxford Brookes, , Birmingham and East Malling research are all recruiting. Further afield, I’ve spotted Arabidopsis post-doc vacancies in Wageningen and Alabama.

There are also two  fully funded workshops open to applications from early career researchers at the moment. Erik Murchie is co-organising a workshop in Thailand (Thailand!) and is looking for post-docs who work on abiotic stress physiology and genetics. Successful applicants will work with rice researchers from Thailand at a 4-day workshop, with the aim of improving understanding of oxidative stress in rice. Apply by 1 May.

Secondly, this synthetic biology summer school in Berlin looks like a great opportunity for PhD students and post-docs working on, or are on the periphery of, synthetic biology. It sounds like an interesting 5 days discussing how to ‘evaluate new techno-scientific areas’ and ‘analyse the societal dimensions of synthetic biology’. As an aside, if you get selected I highly recommend the Alternative Tour of Berlin – it might even give you some ideas for the workshop! This one is a tight deadline, applications close on 10 March.

All of these, including the job at Warwick, for which the advertiser is across the corridor from me, crossed my path on Twitter. If you’re looking for a job or training opportunities and/or want to keep up with news from the community, Twitter is definitely a good place to start. Just follow the right people – try the GARNet accounts (obviously! Me, Lisa, Ruth) and also Mary Williams, Anne Osterrieder, BSPP and UKPSF. Anne even has lists of categorised tweets, a great place to find relevant Twitter users.

You can just use Twitter for harvesting information. You don’t even have to fill out your profile, though you do need a username. But it can be a valuable tool for networking and the ‘branding’ that careers advisors sometimes talk about. Anne has a great paper in Plant Methods about how to use social media as a plant scientist. I use it to share plant science and occasional sci-fi links I come across that I think others will find interesting – if I read an article or paper, attend a good talk, or see a plant science job opportunity or conference.

Register now for GARNet’s 2014 events

We have been busy arranging two great events for 2014! Registration for both Software Carpentry for Plant Scientists (9-10 April) and Arabidopsis: The Ongoing Green Revolution (9-10 September) is now open.


On 9-10 April we are hosting a Software Carpentry bootcamp for plant scientists – an Introduction to Programming for Biologists. For those of you who don’t know about Software Carpentry, it is a foundation that teaches good practice in scientific computing, with the aim of providing all scientists with basic, but reliable and transferable, programming skills. If you’ve ever run through the rain to Computing to have a large ChIP-chip dataset split so you can attempt an Excel analysis on it, you’ll know how valuable that is (based on real events – feel free to insert your own experiences there …)!

We’ve worked with the Software Sustainability Institute to develop a programme suitable for both complete beginners and scientists how know their way around the Terminal/Command Prompt but want to improve their skills and learn how to write reliable, re-usable code they can share with their colleagues and collaborators. Registration is £50 and discounted on-campus accommodation is available.


Later in the year, the GARNet general meeting is returning for one time only on 9-10 September at the University of Bristol. Our theme is ‘Arabidopsis: The Ongoing Green Revolution’. We have a line up of excellent speakers, including plenary talks from Alistair Hetherington (University of Bristol), Andrew Millar (University of Edinburgh), Rob Martienssen from Cold Spring Harbor Laboratories, and Paul Schulze-Lefert and Maarten Koornneef from the Max Planck Institute for Plant Breeding Research. 

The full line-up and registration details can be found by visiting More information will appear on there closer to the time of the conference. Registration costs £150 for two days, lunch and refreshments on both days, and a drinks reception on the afternoon of 9 September. We’d also love to see you at our conference dinner on the evening of the 9 September at the Bristol Marriott Royal Hotel (£44 per head for three courses and wine on the tables).

Collaborations and training in integrative biology

The prevalence of first systems and then synthetic biology in BBSRC and wider UK research funding calls, the establishment of The Genome Analysis Centre (TGAC), the fact that the term ‘big data’ is mentioned in nearly every meeting of any type about the biological sciences … all these point to the irreversible integration of mathematics into biology.

This blog post is for two groups of people: plant scientists who feel they lack the expertise to confidently maneuver in the world of integrative biology; and theoreticians either interested in plant science, or who would rather not have to spend quite as much time dealing with the mathematical problems of the plant scientists in their professional or non-professional circles. (more…)

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