20- 21 May at Tjärnö (and by Jabber)
At this workshop we will focus on how phenotype data for large sets of individuals are stored, shared and organized in tailor-made databases.
Luciano Fernandez is BILS expert in databases and data integration and will together with Anders Blomberg lead the workshop. Note that this workshop is back-to-back on the IMAGO Genome workshop at Tjärnö, 19-20 May.
Overview and aim of the workshop
This workshop will provide an overview of various phenotyping technologies and the corresponding computer-based methodologies to handle and analyse trait data. In particular, it aims to exemplify methodologies where data gathering is automated and performed on a large scale (many individuals; many different traits).
The design of the workshop is to allow for as much time for discussions as for presentations. This means that if you have been allocated a 30 minutes slot in the programme the presentation should be for 15 min and the discussion for 15 min. So, make sure not to make the presentations too long.
The goal of this workshop is to discuss future phenotyping activities and to produce a white-paper for the future development of phenomics for marine organisms at GU. In particular, but not exclusively, the discussion will focus on the IMAGO species for which we currently are generating genome information. The topics in the white paper will address the following items (and maybe more): i) various essential technologies missing at the moment and thus on the wish-list, ii) what technological strategies could be used/be generic for several marine species, iii) the option of measuring phenotypic traits in nature and in the lab, iv) how we can make sure that all this phenotypic information should be handled and accessed by outside users, and v) how can we optimize future studies of the link between genotype and phenotype.
13.00-13.30 General overview on phenomics – technologies, international initiatives and examples of databases (Anders Blomberg)
GROWTH RATE SESSION
13:30 – 14:00 Feature extraction from yeast growth curves – the PRECOG software (Luciano Fernandez)
14.00-14.30 Characterising growth of populations of Skeletonema (Luciano Fernandez)
14:30 – 15:00 Growth rate estimates for Balanus improvisus (Anna-Lisa Wrange)
15:30 – 16:00 The yeast phenomics data base (PROPHECY)(Luciano Fernandez)
SIZE, COLOUR, ETC SESSION
16:00 – 16:30 Measuring various phenotypic traits on Littorina saxatilis (Kerstin Johannesson)
16:30 – 17:00 A first example of a database for Littorina saxatilis (Luciano Fernandez)
17:00 – 17:30 MS-based metabolomics on Fucus and other marine organisms (Göran Nylund)
17:30 – 18:00 Image-based tracking – sperm and cyprid mobility (Jon Havenhand)
18:00 – 18:15 The scared-snail phenotype (Kerstin Johannesson)
FOOD FOR THOUGHT DURING THE DINNER
18:15– 18:30 The PhenoDay conference on automation in plant phenotyping (Luciano Fernandez)19.00 Dinner
8:30 – 9:00 Technologies for morphology-feature-extraction from images (Torbjörn Lundh)
9:00 – 9:30 Phenotype –to- genotype mapping for nitrogen-source dependent traits in yeast (Simon Stenberg)
DISCUSSION AND PLANNING FOR THE FUTURE SESSION
9:30 – 11:00 (with Fika 10:00) Species by species discussion over what phenotypic data we will use and how it should be organized for all the IMAGO species What types of technologies are we lacking? Join forces with other marine centres? We should summarize for each species what we want to achieve and which are the needs. (Species coordinators).
11.00-12.00 Workshop summary - presentation of conclusions from species discussion. What is the next step? Joint applications? How to organize the work? A white paper. (Anders & Luciano)
Anders, Luciano & Kerstin