Hybrid Training School in Gene Annotation
& Manual Curation of the Grape Reference Genome
28th June to 1st July 2022
Photographic Testimonials
Trainers & Expert Trainees
Pre-start Lecture
PARTICIPANT STATISTICS
OVERVIEW
TITLE: Annot’Training – Hybrid Training School in Gene Annotation & Manual Curation of the PN40024 Grape Reference Genome
DATE:
June 28th– July 1st 2022
VENUE: CITA Aragón and CIHEAM, Zaragoza, Spain
BRIEF PROGRAM:
The Annot’ Training School will teach a group of Expert Trainees how to perform manual annotation of grapevine genes from the reference genome using the Apollo Genome Annotation Viewer and Editor, following guidelines developed during the INTEGRAPE workshop held at Colmar in 2021. These Expert Trainees will also be trained in the dissemination of the annotation procedure, which will be practiced with a group of Online Trainees from around the world in an online format during the second half of the Training School.
The Training School will be used for in situ application of the set of best practices for grapevine genome annotation. The two-part sessions will work in a “train-the-trainer” approach to provide researchers from the grapevine community with the opportunity to replicate the outcomes of the Training School in their own environment. The work will be disseminated through the website (http://www.integrape.eu), social media (Facebook, Twitter), as well as through webinars and at the XIII International Symposium on Grapevine Breeding and Genetics in Landau, Germany in 2022.
OUTPUT
GREAT was introduced to the grapevine community during the METHADA eHandsOn Training School and since then, the interface counts 37 users from 13 different countries.
The Working Group Meeting in Colmar was organized in June 2021 and the Apollo interface used for manual curation of the PN40024.v4.1 genes was set up. During this event, the group of experts in manual curation drafted dedicated guidelines. These guidelines were tested during the Working Group Meeting in Valencia in July 2021 and then disseminated and applied to teach 50 trainees during the Annot’Training School in Zaragoza.
SELECTION CRITERIA OF EXPERT TRAINEES (IN-PERSON ATTENDANCE 28 June to 1 July 2022)
- APPLICATIONS CLOSED
DEADLINE for APPLICATION: 15th of May
Evaluation of applicants will be based on the following criteria:
– Postdocs, PhD students, PIs and bioinformaticians working with computational biology related to grapevine with high motivation in spreading these good practices learned during the training school.
– Expert Trainees must have experience in the use of databases, genome browsers and in general, have used genomics data.
A maximum of 10 Expert Trainees will be selected from Participating COST Countries, and will attend the Training School in presence. COST Association will provide a subsidy for travel, accommodation and meal expenses. More info available soon.
Selection of Expert Trainees will be made by COST Integrape local organisers on the basis of all submitted data:
- Reason for participating
- Curriculum vitae
SELECTION CRITERIA OF ONLINE TRAINEES (ONLINE ATTENDANCE 30 June to 1 July 2022)
- APPLICATIONS CLOSED
DEADLINE for APPLICATION: 30th of May
Evaluation of applicants will be based on the following criteria:
– Postdocs, PhD students, PIs and bioinformaticians working with computational biology related to grapevine with high motivation in spreading these good practices learned during the training school.
– People interested in gene annotation and gene family studies.
Online Trainees will be allocated to morning or afternoon sessions based on their geographical location.
Australasia and Europe/Africa: 10 Online Trainees to be selected (morning sessions 30th June and 1st July 2022)
Americas and Europe/Africa: 10 Online Trainees to be selected (afternoon sessions 30th June and 1st July 2022)
Selection of Online Trainees will be made by COST Integrape local organisers on the basis of all submitted data:
- Reason for participating
- Curriculum vitae
PROGRAM
Module 1
Module 2
Objective: Using the “Train-the-trainer” approach, Trainers will train the Expert Trainees who will in turn train the Online Trainees.
A pre-recorded Introductory Lecture will be provided before the Training School takes place and will be mandatory for Expert Trainees and Online Trainees to attend this beforehand.
The manual curation guidelines will also need to be read before the Training School takes place, at: https://integrape.eu/resources/data-management/
The training sessions of Module 1 will be conducted for the 10 Expert Trainees only in the presence of Trainers. Module 2 will involve Trainers, Expert trainees and Online Trainees
Module 1: Train the Expert Trainee
Session 1 (June 28th)
- Introduction summarising the main points of the lecture regarding PN40024.v4 assembly, PN40024.v4.1 gene annotation, the goals of performing manual curation and the manual curation guidelines.
- Getting familiar with the JBrowse/Apollo interface, the different tracks and the various tools to perform accurate manual curation.
- Assign a set of genes to each Expert Trainee to perform manual curation under the supervision of the Trainers.
Session 2 (June 29th)
- Ongoing manual curation for the Expert Trainees to gain expertise (under the supervision of Trainers).
- Share and work collectively on difficult cases that the Expert Trainees may find.
- Train-the-trainer section: share the slides that were used by the Trainers during Session 1 with the Expert Trainees and discuss the essential steps of annotation training.
Module 2: Train the Online Trainee
Session 1 (June 30th)
- Each Expert Trainee will be in charge of teaching manual curation to one Online Trainee in the morning and one in the afternoon (Trainers will supervise 2 Expert Trainees each).
- Assign a set of genes to each Online Trainee to perform manual curation under the supervision of an Expert Trainee (who is in turn under Trainer guidance).
Session 2 (July 1st)
- Expert Trainees will help and supervise Online Trainees to gain expertise with manual curation (under Trainer supervision).
- Complete program soon
CONTACTS
Camille Rustenholz
INRAE
Jérôme Grimplet
CITA-Aragon
Camille Rustenholz
INRAE Colmar- University of Strasbourg
28 Rue de Herrlisheim, 68000 Colmar, France,
camille.rustenholz@inrae.fr
Jérôme Grimplet
Centro de Investigación y Tecnología Agroalimentaria de Aragón
Avda. Montañana 930
50059 – Zaragoza, Spain
Phone: +34 976 71 3635
jgrimplet@cita-aragon.es
Other Trainers in Gene Annotation & Manual Curation
David Navarro-Payá
José Tomás Matus
Luis Orduña
Institute for Integrative Systems Biology, Valencia, Spain