The Assemblathon 2 paper is the winner of the 2013 BioMed Central award for Open Data
Our paper has won the 2013 award for Open Data (sponsored by Lab Archives), an award that is defined as follows:
This award recognizes institutions which have done most to show leadership in taking steps to expand access to the published results of scholarly research.
The citation for this award reads:
An offshoot of the Genome 10K project, and primarily organized by the UC Davis Genome Center, Assemblathons are contests to assess state-of-the-art methods in the field of genome assembly. Assemblathon 2 used real data from three vertebrate species and started in June 2011. The manuscript was published in July 2013.
The following teams submitted one or more assemblies to the Assemblathon 2 project: CSHL team: P Baranay, S Emrich, MC Schatz; MLK team: MD MacManes; ABL team: H Chitsaz; Symbiose team: R Chikhi, D Lavenier, G Chapuis, D Naquin, N Maillet; Ray team: S Boisvert, J Corbeil, F Laviolette, E Godzaridis; IOBUGA team: TI Shaw, W Chou; GAM team: S Scalabrin, R Vicedomini, F Vezzi, C Del Fabbro; Meraculous team: JA Chapman, IY Ho, DS Rokhsar; Allpaths team:S Gnerre, G Hall, DB Jaffe, I MacCallum, D Przybylski, FJ Ribeiro, T Sharpe, S Yin; CBCB team: S Koren, AM Phillippy; PRICE team: JG Ruby; SOAPdenovo team: R Luo, B Liu, Z Li, Y Shi, J Yuan, H Zhang, S Yiu, T Lam, Y Li, J Wang; Curtain team: M Haimel, PJ Kersey; CoBiG2 team; Bruno Miguel Vieira, Francisco Pina-Martins, Octávio S. Paulo; BCM-HGSC team: Y Liu, X Song, X Qin, H Jiang, J Qu, S Richards, KC Worley, RA Gibbs; ABySS team: I Birol, TR Docking, SD Jackman; Phusion team: Z Ning; CRACS team: NA Fonseca; SGA team: JT Simpson, R Durbin; Computer Technologies Department (CTD) team: A Alexandrov, P Fedotov, S Melnikov, S Kazakov, A Sergushichev, F Tsarev: Newber-454 team: JR Knight.
The resulting assemblies were assessed by teams from the Wellcome Trust Sanger Institute (M Hunt, T Otto), UC Santa Cruz (D Earl, Paten B) and UC Davis (K Bradnam, J Fass, I Korf). Resources (sequences, fosmids, and optical maps) were generated and validated by E Jarvis, S Zhou, S Goldstein, M Place, DC Schwartz, M Bechner, J Shendure, J Kitzman, J Hiatt, J Howard, G Ganapathy, and G Zhang. The principle organizers behind Assemblathon 2 were David Haussler, Ian Korf, and Erich Jarvis.
Thanks to everyone involved in generating data, submitting assemblies, and helping write the paper. I’d also like to specifically thank all of the co-authors for supporting our decision to use the arxiv preprint server, and for agreeing to submit the final paper to Gigascience which also allowed us to publish the data (including all of the submitted assemblies) as citable datasets in GigaDB.
Open science FTW!
2014-04-22 18.28 - Updated to include mention of award sponsor.