GARNet Committee Meeting Minutes: September 8th 2016
26th Sep 2016
Please view the public minutes from the GARNet Advisory Committee Meeting that took place at the Cardiff University in September 2016.
GARNet2016 CRISPR-Cas Workshop
20th Sep 2016
Introduction to CRISPR-Cas, troubleshooting target design and verification of mutants.
Organisers: Vladimir Nekrasov and Amanda Hopes
1. Introduction on CRISPR/Cas as a tool for genome editing
2. Construct assembly methods
3. Target selection and ways to reduce off-targets
4. Ways to detect mutations
5. Case studies:
- CRISPR/Cas in model and crop plants
- CRISPR/Cas in diatoms
GARNet2016 Araport Workshop
20th Sep 2016
Usage and Application development within Araport.
This hands-on workshop is aimed at users of the web portal and will cover the two main applications - ThaleMine and JBrowse.
Organisers: Chris Town and Sergio Contrino
- Content and origins of the various data sets that can be accessed through the gene-info pages.
- Making and using lists, including the tools/widgets that operate on lists.
- Templates (pre-formed queries) and how they can be modified to an individual’s needs.
- Query Builder that provides a graphical interface to build, save and share SQL queries.
- App Store to get a feeling for what Apps are and how they can be built.
- Review the wide range of tracks available and the sources of the data as well as the ways in which data can be searched and manipulated within the application.
- Demonstrate how to import your own data as tracks into JBrowse and review plans for a more user-friendly mechanism for track sharing that is under development.
GARNet2016 Workshop: Finding your Arabidopsis Gene in Wheat
20th Sep 2016
The workshop consisted of 5 parts:
- - Introduction to the Wheat Genome
- - Finding your Arabidopsis Gene in Wheat
- - Wheat Gene Expression Browser
- - In silico TILLING in Wheat
- - Additional Training Materials
All these materials are available at:
- where you will find powerpoint files and youtube videos of the presentation they gave at the meeting. Thanks to the speakers for making this outstanding resource available.
- We include a PDF of the entire presentation here but as some of the transitions are lost in this document, I might recommend downloading individual powerpoint files from the above URL.
GARNet2016: Innovation in the Plant Sciences
5th Sep 2016
In September 2016, Cardiff University hosted the latest biennial GARNet meeting that brought together 100 delegates to learn about and discuss the newest innovations in plant science.
The meeting included five plenary sessions on:
- Frontiers in Plant Imaging
- Enabling the Translational Pipeline
- Plant Synthetic Biology
- Genomics tools for Gene Discovery
- Cell Signaling
as well as three workshops entitled 'Finding your Arabidopsis Gene in Wheat', 'Troubleshooting experiments with CRISPS-Cas9 and 'Usage and Application development within Araport'.
Please download and take a look at the abstract book to learn about the exciting science that occured at this event.
GARNet Committee Meeting Minutes: June 2016
16th Jun 2016
Please view the public minutes from the GARNet Advisory Committee Meeting that took place at the University of Bristol in June 2016.
GARNet/Egenis meeting on 'Integrating Large Data into Plant Science: From Big Data to Discovery'
21st Apr 2016
GARNet and the Exeter Centre for the Study of the Life Sciences (Egenis) are excited to host a two-day workshop on ‘Integrating Large Data into Plant Science: From Big Data to Discovery’ to be held in the picturesque Dartington Hall in Devon on April 21st-22nd 2016.
The aims of this workshop are to:
1. Introduce examples of how researchers have re-used datasets in innovative ways.
2. Examine the intrastructure that exists to support the re-use of large datasets
3. Discuss the mechanisms by which the community deals with big data.
Please download the abstract book and look out for a meeting report coming in the near future.
GARNet/OpenPlant CRISPR Workshop
24th Sep 2015
GARNet and OpenPlant were delighted to invite over 140 attendees to the CRISPR-Cas workshop held at the John Innes Centre at the start of September 2015, sponsored by Plant Methods. This workshop was designed to introduce CRISPR technology and highlight what might be possible with his transformative technology. A report from the meeting can be found on the GARNet blog.
On Day Two of the workshop we hosted ~20 researchers to learn more detail about the basic principles for use of CRISPR-Cas technology. The workshop was split into the following parts: 1. Designing guide RNAs. 2. Making constructs using the MoCLo system. 3. Screening trangenic plants.
This workshop was run by Dr Nicola Patron and she is happy to share her notes from that session, which can be downloaded below. This will hopefully give some guidance to anyone embarking on use of CRISPR-Cas for the first time.
Data Mining with iPlant
20th Oct 2014
In September 2013, GARNet hosted a training workshop at the University of Warwick. The four-day 'Data Mining with iPlant' workshop gave delegates comprehensive training in how to use the iPlant Collaborative's cyberinfrastructure for storing, sharing and analysing 'Big Data' in plant science.
You can read more about this workshop by visiting our blog post about it. We also featured it in the December 2013 issue of GARNish (click download link below) and the Wiki-style materials used during the workshop can be found here: https://pods.iplantcollaborative.org/wiki/display/Events/Data+Mining+with+iPlant.
Following this workshop, we wrote and submitted a workshop report to the Journal of Experimental Botany, which I am pleased to say has now been published.
Martin L, Cook C, Matasci N, Williams J and Bastow R (2014). Data Mining with iPlant: A meeting report from the 2013 GARNet workshop 'Data Mining with iPlant', Journal of Experimental Botany, DOI: 10.1093/jxb/eru402 can be accessed via this toll-free link.
High-throughput sequencing technologies have rapidly moved from large international sequencing centres to individual laboratory benchtops. These changes have driven the ‘data deluge’ of modern biology. Submissions of nucleotide sequences to GenBank, for example, have doubled in size every year since 1982, and individual data sets now frequently reach terabytes in size. While ‘big data’ present exciting opportunities for scientific discovery, data analysis skills are not part of the typical wet bench biologist’s experience. Knowing what to do with data, how to visualize and analyse them, make predictions, and test hypotheses are important barriers to success. Many researchers also lack adequate capacity to store and share these data, creating further bottlenecks to effective collaboration between groups and institutes. The US National Science Foundation-funded iPlant Collaborative was established in 2008 to form part of the data collection and analysis pipeline and help alleviate the bottlenecks associated with the big data challenge in plant science. Leveraging the power of high-performance computing facilities, iPlant provides free-to-use cyberinfrastructure to enable terabytes of data storage, improve analysis, and facilitate collaborations. To help train UK plant science researchers to use the iPlant platform and understand how it can be exploited to further research, GARNet organized a four-day Data mining with iPlant workshop at Warwick University in September 2013. This report provides an overview of the workshop, and highlights the power of the iPlant environment for lowering barriers to using complex bioinformatics resources, furthering discoveries in plant science research and providing a platform for education and outreach programmes.
GARNet 2014 - Arabidopsis: The Ongoing Green Revolution
15th Oct 2014
GARNet hosted its conference, Arabidopsis: The Ongoing Green Revolution, at the University of Bristol on 9th and 10th September 2014. You can read more about the conference by clicking here, find a Storify of tweets here, or view some photos from the event on our Weeding the Gems blog here.
Below is the programme of speakers we enjoyed over the two days. To download presentations from some of these speakers, please visit our blog: http://blog.garnetcommunity.org.uk/garnet-2014-presentations/.
Clicking the Download link below will take you to the conference abstract book.
Session 1: Physiology & Productivity
- Alistair Hetherington, University of Bristol: The response of stomata to environmental signals
- Miriam Gifford, University of Warwick: Understanding plant root developmental plasticity using cell-specific genomes
- Steve Penfield, University of Exeter: A cryptic switch formed by external temperature coincidence generates a life history strategy for Arabidopsis
- Beatriz Lagunas, University of Warwick: The AtSCL26 transcription factor controls cross-talk between GA- and Nitrogen- control of root architecture in Arabidopsis thaliana roots
Session 2: Genome Biology
- Siobhan Brady, University of California, Davis, USA: Getting to the root of things: spatiotemporal gene regulatory networks in plant roots
- Ian Henderson, University of Cambridge: Unravelling interactions between genetic diversity and recombination in Arabidopsis
- Antony Dodd, University of Bristol: Circadian signalling between subcellular genomes
- Emily Hawkes, John Innes Centre: Evolutionary conservation of an Arabidopsis long non-coding RNA, COOLAIR, supports a regulatory function
Session 3: Natural Variation
- Maarten Kournneef, Max Planck Institute for Plant Breeding Research, Germany: Exploring Arabidopsis natural variation
- Adrian Brennan, University of Durham: Population genetic strcuture and natural variation of the model plant Arabidopsis thaliana in its native southern range extremes
- Javier Agusti, University of Oxford: Using natural variation to identify new cambium regulators
- Monika Mierzwinska, University of Aberdeen: Natural variation in endodermal development and plant mineral nutrient homeostasis
- Andrew Millar, University of Edinburgh: Systems for biological timing in the green cells
- Siobhan Braybrook, The Sainsbury Laboratory, Cambridge: Understanding the physical basis of growth from the top down
- Leah Band, University of Nottingham: Systems analysis of auxin transport in the Arabidopsis root tip
- Matthew Hindle, University of Edinburgh: The reduced kinome of Ostreococcus tauri: core green lineage signalling components in a tractable model species
Session 5: Plant Interactions with their Environment
- Paul Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Germany: Functions of the Arabidopsis bacterial root microbiota in plant health
- Cyril Zipfel, The Sainsbury Laboratory, Norwich: Regulation of early receptor kinase-mediated immune signalling
- Kerry Franklin, University of Bristol: Sunlight, photoreceptors and plant development
- Sophie Berckhan, University of Nottingham: Why do plants sense oxygen?