News

SDSC Gordon Info

Everyone who applied for SDSC Gordon compute time for the map challenge will receive an initial allocation of 22,000 service units per proposed target. Altogether 14 users plan to perform a total of 45 reconstructions. Some useful links:

Other things to be aware of:

SDSC Offers Supercomputer Resources; Map Challenge Submission Deadline Extended

Nov 9, 2015: We have two major announcements regarding the ongoing EMDataBank Map Challenge.

First, the San Diego Supercomputing Center (SDSC) is generously offering supercomputing resources to support the Map Challenge.  The resources, made available through an SDSC Director’s Discretionary Award, include 1 Million core-hours on SDSC Gordon and 20TB of sandbox data storage on Gordon’s parallel file system Data Oasis.

Announcing the 2nd EMDataBank Model Challenge

EMDataBank is pleased to announce the 2015/2016 Model Challenge.

All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.

Benchmark targets of varying size and complexity have been selected from recently deposited 3DEM structures based on current state-of-the-art detectors and processing methods, in the resolution range 2.2-4.5 Å.

Announcing the 2015 EMDataBank Map Challenge

EMDataBank/Unified Data Resource for 3DEM is pleased to announce the 2015 Map Challenge.

All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.

Seven benchmark raw image datasets have been selected for the challenge. Six are selected from recently described single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images.

Pages

Map Challenge

June 2017: The Blind Assessment Phase has ended and full submission data are now available.  Please visit the map challenge page for more details.

Model Challenge

The Assessment Phase for the 2015/2016 Model Challenge is open. Please visit the model challenge page for more details.

Welcome

 Three-dimensional Electron Microscopy (3DEM) is becoming a key experimental method in Structural Biology. Recent advances in image acquisition and processing are yielding more structures determined at near-atomic resolution, as well as a wide range of macromolecular complexes and subcellular architectures determined at lower resolution.

 

A major goal of the EMDataBank team is to work with the 3DEM community to establish data validation methods that can be used in the structure determination process, define key indicators of a well-determined structure that should accompany every structure deposition, and implement appropriate validation procedures into a 3DEM validation pipeline. Following recommendations of the EM Validation Task Force (Henderson et al 2012), we are hosting new benchmark challenges here, with aim to stimulate further community discussions about validation procedures for 3DEM maps and map-derived models. Prior community-organized 3DEM challenge activities have included a Particle Picking Challenge (Zhu et al 2004),  CryoEM Modeling Challenge (Ludtke et al 2012), and CTF Challenge (Marabini et al 2015).

EMDataBank Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to challenges@emdatabank.org

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