ContentMine Workshop & Hackathon at TGAC: mining for synthetic biology

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Supported by the OpenPlant Fund

Interested in using mining technologies for synthetic biology?

Content mining technologies hold much potential for maximising scientific discovery and the reuse of research through automated searching, indexing and analysing of scientific literature.

In this workshop, we aim to educate and engage technologists and biologists who are interested in using mining technologies for synthetic biology; to better enable access to research literature and data in plant synthetic biology.

The hackathon on Day Two aims to improve searching and indexing of plant synthetic biology texts through open source technology platforms developed by the Grassroots Genomics project at TGAC and the ContentMine platform from the University of Cambridge.

Target Audience

Best suited to biologists and bioinformaticians who have some experience of using command line tools or the enthusiasm to pick this up! As such, formal programming experience is not a requirement, but you may find it useful to attend the Software Carpentry Bootcamp held at TGAC prior to this event.

Course prerequisites: Basic prior knowledge of programming concepts.

Course details

The registration fee is £50.00 (plus booking fee of 2.13 per cent) – refundable on attendance (minus booking fee) which will be processed post event.

We are also able to reimburse up to two nights accommodation with a limit of £80.00 per night (receipts required).

Scientific Organisers:

Emily Angiolini, The Genome Analysis Centre (TGAC), UK Rob Davey, The Genome Analysis Centre (TGAC), UK Richard Smith-Unna, University of Cambridge, UK

Course Faculty:

Rob Davey, The Genome Analysis Centre (TGAC), UK Richard Smith-Unna, University of Cambridge, UK

Further Details:

Venue: The Genome Analysis Centre (TGAC), UK Application deadline: Friday 26 February 2016 Participation: First come, first served

OpenPlant Fund now open for applications! Deadline 4 March 2016

The OpenPlant Fund will support innovative, open and interdisciplinary projects relevant to plant Synthetic  Biology over 2015-19. Around 20 six-month projects per year will receive £4k each, with an  additional £1k awarded on completion for follow-on and outreach. The first round of applications for 2016 is now open and will close on 4 March!

The aim of the fund is to promote the development of plant Synthetic Biology as an interdisciplinary  field and to facilitate exchange between The University of Cambridge, the John Innes Centre and The Sainsbury Laboratory for the development of open technologies and responsible innovation in the context of Synthetic Biology.

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Applicants should be graduate students or postdoctoral workers at the University of Cambridge, the John Innes Centre or The Sainsbury Laboratory. The team must be interdisciplinary, must contain members from both Norwich and Cambridge and may contain external collaborators of any type. Applicants must have agreement from their research supervisor and cost-code sponsor that the  proposed project and management of the allocated funding will fit with their existing work. All proposals must lead to tangible, publicly documented and open outcomes, which could include (but are not limited to) the following:

• Design files and prototype for a hardware project
• Software development and documentation
• White paper arising from a workshop
• Educational resource
• Synthesis and sharing of useful DNA parts or vectors.

For more information and to apply see the OpenPlant Fund webpage.

OpenPlant Supported TReND/icipe bioinformatics workshop

RICHARD SMITH-UNNA DELIVERING A PLANT SYNTHETIC BIOLOGY SESSION AT ICIPE

The OpenPlant Fund supported TReND in Africa to include plant synthetic biology in their recent bioinformatics course held at icipe in Kenya. The course was a great success with 35 students selected from a total of 430 applicants. They learnt R and Unix programming basics, as well as advanced genomics techniques from a number of different areas of biology.

The plant synthetic biology session was delivered by Richard Smith-Unna (@blahah404), a PhD Student in the OpenPlant-affiliated Hibberd Lab at the Department of Plant Sciences, University of Cambridge.

TReND’s Jelena Aleksic recorded interviews with participants who described their experience of the course, you can view the playlist below and find more about TReND in Africa’s activities on their website.

Plant synthetic biology lecture at @icipe! Thank you @_OpenPlant for supporting #trendngs15 @TReNDinAfrica pic.twitter.com/NKs8BWC1fV

— Jelena Aleksic (@firegenome) December 4, 2015