Software

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Peer Review

[Data &  Software] Peer review is fundamentally a cooperative process between scientists in a community who agree to review each other’s work in an unbiased fashion. Peer review is the foundation for decisions concerning publication in journals, awarding of grants, and academic promotion. We performed a laboratory study of open and closed peer review based on an online game. We showed that when reviewer behavior was made public under open review, reviewers were rewarded for refereeing and formed significantly more cooperative interactions (13% increase in cooperation, P = 0.018). We also show that referees and authors who participated in cooperative interactions had an 11% higher reviewing accuracy rate (P = 0.016). Our results suggest that increasing cooperation in the peer review process can lead to a decreased risk of reviewing errors. The paper was written by Jeff Leek, Margaret Taub and Fernando Pineda

Kinetic Modeling of toxoplasma Gondii

[CompModel] The phylum Apicomplexa includes parasites responsible for diseases such as malaria, cryptosporidiosis, and toxoplasmosis. The latter disease is caused by the Toxoplasma gondii parasite. Like all parasites in this phylum, Toxoplasma gondii reproduces inside the cells of its hosts. Thus, host cell invastion is an essential step of the T. gondii life cycle. Characterizing the stages of host-cell invasion, has traditionally involved tedious microscopic observations of individual parasites over time. As an alternative, we introduced the use of mathematical models to interpret observations of entire synchronized populations of invading parasites. The paper was written by Björn Kafsack, Vern Carruthers and Fernando Pineda. It was based on a Bioinformatics Capstone project by Björn Kafsack.

Detecting non-coding RNA

[zcalc] Zcalc is a fast implementation of di-nucleotide z-score that scores sequences for detecting non-coding RNA.