APAeval is continuing!
As we received lots of positive feedback after our successful hackathon @RNA2021, we decided to continue working on APAeval. Read more about our work in our status update published after the hackathon. If you’re interested to join in any form, just reach out to us at apaeval@irnacosi.org or check out our Github page.
Everybody is welcome (deadlines and prerequisites mentioned below no longer apply) and we’d be very happy to hear from you!
A community effort to evaluate computational methods for the detection and quantification of poly(A) sites and the estimation of their differential usage across RNA-seq samples.
Organizers
Dr. Mihaela Zavolan, University of Basel
Dr. Yoseph Barash, University of Pennsylvania
Questions about APAeval? Contact us at apaeval@irnacosi.org
Sponsor
Background:
Many labs within the RNA community rely on computational methods for detecting and quantifying poly(A) sites and their differential usage across samples from RNA-seq data. However, no comprehensive evaluation of such methods has been carried out so far, which makes it tedious for users to choose the appropriate tool and evaluate the impact of implementation choices on the output.
Therefore, we are organizing a community effort to evaluate existing methods during the 2021 RNA Society Meeting, with the aim of providing a benchmark for further development, validation and application of these methods.
RNA 2021 will be held virtually from May 25th to June 5th. Any interested RNA Society member is welcome to join this effort by contributing to one of the teams listed below.
How to participate:
Bonus:
Up to ten most active contributors in APAeval will be awarded a travel fellowship at the RNA Society meeting 2022!
Prerequisite: Participants need to register for an RNA Society membership (Starting from $36 per year). 20 selected participants will receive a $50 amazon gift voucher after the event, so yes, you can even earn an amazing $14 (and the travel fellowship, and the co-authorship, not to mention the fun)!!
The Committee
You are interested in genomics and computational analysis and would like to help organize this event? You will be on a committee composed of trainees (students/postdocs), mentored and guided by two members of the organizing committee for computational challenges – Dr. Mihaela Zavolan and Dr. Yoseph Barash. This committee will assemble prior to the RNA 2021 meeting, starting with virtual meetings in April 2021, and will be responsible for:
- Defining suitable test datasets – these datasets could come from the literature, but could also be produced specifically for this grand challenge. They should include RNA-seq data for the inference, and orthogonal data sets, generated with other approaches, for validating predictions.
- Defining the evaluation metrics.
- Collecting the methods to be benchmarked.
- Drafting the summary of results for
- a presentation at the RNA Society meeting 2021
- a manuscript authored jointly by the contributors to this challenge.
Register until April 15th, 2021!
The Evaluation Team
You are interested in running bioinformatics tools, scripting or preparing beautiful visualizations with like-minded people? You will be virtually hacking together during the RNA society meeting, from May 25th to June 5th 2021. Participants will be responsible for:
- Setting up a common code repository
- Performing evaluation tasks on the methods included in this challenge
- Developing scripts and/or pipelines to present and compare the evaluation output
- Drafting the summary of results for
- a presentation at the RNA Society meeting 2021
- a manuscript authored jointly by the contributors to this challenge.
Register until May 24th, 2021!
The Special Agents
You like the idea of APAeval but don’t know how you could contribute? You want to be on all teams at once but not really? You just want to give an important hint and then be out of here? You’re an APA ninja (or a unicorn)?
Great! Just drop us some lines about your interests and your expertise and we’ll see how to fit you in.
Register until May 24th, 2021!
The Method Team
You are a method developer and would like to see your method included in the benchmark? Or you are an experienced user who would like to ensure that your method of choice is evaluated? While the evaluation aims to be as independent as possible, you are most welcome to suggest a method and consult with the organizing and evaluation teams to make sure that the method is run and interpreted as intended.
Register until May 17th, 2021!
Expected outcomes of APAeval:
- Extensive benchmark of existing methods for detecting and quantifying poly(A) sites and their differential usage across samples from RNA-seq data
- Presentation at the end of the RNA Society Meeting
- Publication of a manuscript describing the results. The organizers will coordinate the effort of submitting the manuscript to the RNA Journal. All participants in APAeval will be acknowledged as contributing authors