The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p

Electrochemical xanthine biosensor based on zinc oxide nanoparticles‒ multiwalled carbon nanotubes‒1,4-benzoquinone composite

Zinc oxide nanoparticles (ZnONPs), multiwalled carbon nanotubes (MWCNTs) and 1,4-benzoquinone (BQ) dispersed in chitosan (CS) matrix were used to construct a xanthine biosensor. Xanthine oxidase (XOx) was immobilized onto BQ-MWCNTs-ZnO–CS composite modified glassy carbon electrode (GCE) using glutaraldehyde as the crosslinking agent. The parameters of the construction process and the experimental variables for the biosensor were optimized. The xanthine biosensor showed an optimum response within 10 s, and the sensitivity was 39.4 μA/mMcm2 at +0.25 V (vs. Ag/AgCl). The linear working range of the biosensor was found to be 9.0×10−7-1.1×10−4 M with a detection limit of 2.1×10-7 M. The biosensor exhibited good long-term stability and reproducibility. The presented biosensor was also used for monitoring the freshness of chicken and beef flesh

Biçimsel yöntemler ile dağılımlı yazılımların doğrulanması ve geçerlileştirilmesi

TÜBİTAK EEEAG COST01.10.1997Gerçek zaman iletişim yazılımlarında kullanılan dagımlı yazılımların betimlenmesi ve doğrulanması için iki ticari SDL ürünü olan SDT (Telelogic) ve GEODE (Verilog) paketleri kullanılarak uygulamalar yapıldı ve yeni teknikler geliştirildi, özellikle Lucent Technologies'de geliştirilmiş olan COSPAN doğrulayıcısının SDL platformunda kullanılabilmesi için SDL-S/R derleyicisi gerçekleştirildi ve SDL dili ile COSPAN doğrulayıcısının donanım/yazılım entegre tasarımı (HW/SW co-design) için genişletilmiş SDL tanımı yapıldı.Bunun yanısıra SDL kullanımında durum patlaması olarak anılan karmaşıklık sorununa çözüm getirmek üzere teknikler geliştirildi.( In order to specify and validate embedded real-time software used in communication systems the commercial products SDT and GEODE were applied to numerous examples and techniques were developed for that purpose. In particular to use COSPAN verifier developed at Lucent Technologies within an SDL platform a restricted SDL to S/R compiler was implemented and SDL was extended as the first step of implementing a HÏV/SW codesign tool using the COSPAN verifier. In addition complexity relief techniques were developed to overcome the problem of state explosion when using SDL)