Minutes of the EPIC meeting in Norwich

Minutes of the EPIC meeting, Norwich October 2013

Doris Wagner discussed the history of EPIC and accomplishments of the RCN so far. Brian Gregory introduced the EPIC CoGe Browser, current and proposed features as well as the current focus on data from Arabidopsis, soybean and rice. A unified epigenome browser was first discussed at the first EPIC meeting in conjunction with the PAG in January of 2011 and took further shape at the Banbury conference later the same year. It was funded for 2 years (initial phase) by the Gordon and Betty Moore foundation and has received computational and infrastructure support from iPlant. Brian Gregory (Upenn/EPIC) and Eric Lyons (iPlant) have been working on development and implementation. Finally Blake Meyers discussed the International Arabidopsis Informatics Consortium (IAIC), its governance plan and the roles of the current advisory board and its relationship to the recently funded Arabidopsis Informatics Portal (AIP). He also described how independently funded modules (such as one spearheaded by Nick Provart) can integrate with AIP.

The discussions can be summarized as follows:

Goals and Deliverables of EPIC

A. Everyone agreed that continued implementation and further development of the EPIC CoGe browser is a high priority that will greatly benefit the epigenetic community. The plan is to upload all Arabidopsis data by the end of the year, some maize and soybean data is also currently being uploaded. Eric and Brian plan to apply for a PGRP grant this March for phase II of the EPIC CoGe browsers for Arabidopsis, corn and soybean. Buy-in from ‘heavy hitters’ in the field is important, apparently the Ecker, Jacobsen and Weigel labs have already signed on. It is envisioned that the raw data will still be desposited at NCBI/GEO as this is viewed as a long-lived repository. Goals for CoGe are development of pipelines for uniform and automated raw data analysis (ChIPseq and RNA seq), upload of all existing datasets, development of a list of parameters to be recorded by all data generators to facilitate across dataset comparisons  (standardization), and development of query and visualization capabilities to allow data analysis and publication figure generation. It is envisioned that the Arabidopsis, maize and soybean CoGe browsers will become modules that interface with AIP.

B. It was also decided that EPIC members from other countries will begin to get financial and personnel support for development of additional CoGe browsers that will be implemented alongside the Arabidopsis, maize and soybean EPIC CoGe’s. China will focus on rice, Korea on a Solanaceae family member, UK/EU on wheat and Brachypodium. Personnel will be trained by Brian and Eric as needed.

C. The group was divided over whether we should try to seek funding from funding agencies and industry to elucidate cell type specific, environment and developmental stage-specific epigenomes (data generation). On one hand this type of funding was viewed as an important catalyst for the field, on the other it was feared that such initiatives are too static and the approaches used and goals stated frequently become obsolete or outdated during the lifespan of the initiative. While some felt that a thorough ‘cataloging’ of marks and chromatin states would enhance all future comparative epigenomics analyses, others felt monies would be better spent on investigating Biology driven questions.

Next meetings/ additional activities

D. EPIC will continue to oversee/coordinate the browser development in collaboration with iPlant. The standing Planning Committee will continue to be involved in this activity and to hold yearly meetings to discuss the browsers and current and future needs of the plant epigenetics community. The transition to an elected EPIC board will occur gradually over the next years. It was unclear whether a new source of funding was required for EPIC to continue to be able to support future meetings and the maintenance of website. This should be clarified at the 2015 meeting.

E. The next EPIC meeting will be held on May 15 2014 (14-15 or 15-16) in Philadelphia and will be comprised of a scientific symposium and an organizational meeting. At this meeting, we envision both Industry and Funding Agency presence. Craig Pikaard and Eric Richards will work on this.

F. Future EPIC organizational meetings will be held in conjunction with a scientific conference, with each yearly conference venue placed in the Americas, Asia or Europe. Scott Michaels will look into Keystone/FASEB/Gordon type conference. The topics will span epigenetics and noncoding RNAs. Xiao-Feng Cao and Zhi-Zhong Gong will investigate the possibility for a future conference to be held in China.

G. The website, although it has many members, has not engendered as much interaction as was hoped. Some immediate improvements can be made, for example the link to the CoGe browser should be clickable. Charis Cook from Garnet has agreed to help provide news items. Vincent Colot and Francois Roudier have been asking authors of epigenomic papers to provide news items. It was suggested that 2 EPIC members guest-edit an issue of ‘Methods’ and solicit new or improved protocols for plant epigenetic research. The abstracts of these articles will then be posted on the EPIC website. Roger Deal and Francois Roudier may spearhead this initiative. Blake Meyers and Brian Gregory have just finished guest-editing a Methods issue on ncRNAs and can provide insight on the process. Teaching tools will be solicited from all EPIC members and a link to those available via The Plant Cell was added on the EPIC website. Advertising EPIC at the PAG, maize and Arabidopsis meetings will continue with one goal being to foster inclusion of breeders, evolutionary biologists and ecologists in this initiative.

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