The meeting will begin with the Bioinformatics Workshop which has previously been very popular. This will be an introduction to on-line resources such as Ensembl/Vega, IKMC/IMPC, GRC, CCDS, MGI and RefSeq/EntrezGene and how they are all tied together. The GENCODE gene set lies at the heart of many of the resources researchers use and we will point users to the many human and mouse ENCODE resources that are available. The ENCODE (encyclopedia of DNA elements) collaboration involves a large number of groups from across the globe working on both experimental and computational aspects of everything related to genes: annotation, structure, expression, regulation, function, etcetera. The mouse ENCODE project applies this to tissues and developmental stages not available for study in human.
The workshop comprises three modules (approximately 1 hour each, with a 15 minute interval in between):
1: Background and Annotation
We will discuss how the GENCODE annotation is created and demonstrate how users can access the resulting data sets through the common channels such as Ensembl, UCSC genome browser and RefSeq and explain the differences between the different annotations offered by these resources. We will also introduce more specialised resources such as GRC (Genome Reference Consortium) and CCDS (Consensus CDS).
[organiser: Laurens Wilming]
2: IKMC - International Knockout Mouse Consortium
The IKMC (now merged into the IMPC, see below) provides the foundation for building a comprehensive functional catalogue of a mammalian genome by generating a knockout mouse strain for every protein coding gene and making them available to the scientific community. We will show how the IKMC creates its knockout models and explain the different types of knockouts.
[organiser: Mark Thomas]
3: IMPC - International Mouse Phenotyping Consortium
The IMPC builds upon the work of IKMC consortium by using IKMC ES cell clones to progress towards its goal of generating and phenotyping a knockout mouse strain for every protein coding gene. We will demonstrate how users can find phenotype data of interest related to gene, phenotypes and disease. The demonstration will include how to download relevant datasets from the mousephenotype.org website and how to download by programmatic access.
[organiser: Terry Meehan]
If delegates have any particular annotation queries about their genes of interest, we are happy to discuss these, either at the end of the workshop or during the conference.
The workshop will be held at the Bar Harbor Club and each participant should bring a laptop if they wish to follow examples during the workshop. There will be no extra cost for participating in the workshop, but places for it must be pre-booked. Please specify if you wish to register for this workshop in section 3 of the registration process.
There will be a satellite meeting on Sunday from 1:30 pm – 6:00 pm specifically for trainees to present oral presentations to an audience consisting mainly of other students and post docs. A selection of these presentations will be asked to present to the main conference and all other trainee presentations will be presented as posters at the main conference. There is no additional cost to attend this symposium, but pre-registration is requested. All scholarship recipients should participate. Trainees, when submitting your abstract within the submission system, please select if you wish it to be considered for the Trainee Symposium in addition to the Main Conference (you will find a tick box within the submission system).
Systems Genetics Workshop
The aim of this workshop is to familiarize current and potential users with two systems genetics platforms and their associated tools. The two reference populations (GRPs) are the Collaborative Cross and Diversity Outbred populations. The course will introduce and facilitate utilization of GRPs to address complex biological questions. Syllabus items include:
- Introduction to GRPs
- Online resources for the CC and DO
- Experimental design with GRPs
- QTL mapping in multi-parent populations, and
- Platform specific considerations when using the CC and DO
A basic familiarity with genetic diversity, quantitative trait genetics and the concept of the Collaborative Cross are suggested for interested participants. The instructors of the workshop are experts in the various aspects of usage, implementation, interpretation and analysis of GRP-derived data, so even interested participants familiar with the usage of GRPs might find the workshop valuable. Each participants is expected to provide his/her own laptop to access the internet. There will be no additional fee to attend this workshop, but participation is limited based on the size of the room and number of instructors. Please indicate your interest on the registration form for the meeting, and the organizers will do their best to accommodate as many individuals as possible while ensuring maximum diversity in the audience based on their lab group affiliations. A certificate will be provided after completion of the workshop.
MGI Hands-on Exploration and Workshop (1.5h)
Take the time to learn about MGI's current features by participating in a hands-on workshop. This will include a short seminar-style demonstration followed by the opportunity to navigate the site using a set of self-guided exercises. Participants will be instructed on how to locate pertinent biological information, perform a variety of searches, try out the Human-Mouse: Disease Connection translational tool and the use the MouseMine computational access platform. User Support will be present to discuss more specific research questions as well. The same workshop will be offered during the poster sessions on Monday and Tuesday and at the MGI Symposium on Friday.
Participants must bring their own laptops.Contact firstname.lastname@example.org with any questions
MGI Symposium 25th Anniversary
There will be a 25th anniversary MGI symposium on 10/30/14 at the LCC Auditorium at the Jackson Lab that you may want to consider attending. For more information on this noteworthy event, please visit http://www.informatics.jax.org/faq/MGI25.shtml