BUSCADOR RECOLECTA

OncodriveFM detects candidate cancer driver genes and pathways from catalogs of somatic mutations in a cohort of tumors by computing the bias towards the accumulation of functional mutations (FM bias).This novel approach avoids some known limitations of recurrence-based approaches, such as the dif?culty to estimate background mutation rate, and the fact that they usually fail to identify lowly recurrently mutated driver genes.

Onexus is a modular framework to manage the complete life cycle of data analyses. Data analyses follow these steps: analysis definition, analysis execution, results storing, results browsing and finally results publishing.

Wok is a workflow management system implemented in Python that makes very easy to structure the workflows, parallelize their execution and monitor its progress among other things. It is designed in a modular way allowing to adapt it to different infraestructures./nFor the time being it is strongly focused on clusters implementing any DRMAA compatible resource manager (i.e. Oracle Grid Engine) which working nodes have a shared folder in common. Other, more flexible infrastructures (such as the Amazon EC2) are considered for future implementations.

Machine-learning based approach to classify cancer driver genes into to Activating or Loss of Function roles for cancer gene development.

Javascript library to create interactive heatmaps within webpages.

HDAC7 is a repressor of myeloid genes whose downregulation in pre-B cells is required for transdifferentiation into macrophages.

Oncodrive-CIS is a method aimed to identify those copy number alterations (CNAs) leading to larger in cis expression changes that may be useful in elucidating the role of these aberrations in cancer. This is based on the hypothesis that a gene driving oncogenesis through copy number changes is more prone to bias towards overexpression (or underexpression) as compared to bystanders. The effect of the gene dosage is assessed by observing expression changes not only among tumors but also taking into account normal samples data, when available./nOncodrive-CIS has several potential benefits: first, it did not examine the frequency of the CNAs across samples and therefore the detection of low-recurrent driver alterations was not impaired. Second, amplifications and deletions were evaluated separately to obtain a fair ranking of genes, because the expression change measured in deletions was lower than the one obtained from multi-copy amplifications. Third, the expression of genes in tumor samples was analyzed according to the copy number status but was also compared to normal samples, thus better revealing the gene misregulation role of CNAs in cancer cells. And finally, it should be emphasized that the relationship between expression changes and their functional impact is complex, thus Oncodrive-CIS is proposed as a method to elucidate the role of CNAs in cancer which may be complementary to analyses based on other criteria.

The effects on growth performance of supplementation of four different AA combinations in a milk replacer (MR, 25.4% CP and 20.3% fat) based on skimmed milk powder and whey protein concentrate were evaluated in 76 Holstein male calves (3 ± 1.7 d old). The 4 MR were: CTRL with no AA supplementation; PG supplying additional 0.3% Pro and 0.1% Gly; FY supplying additional 0.2% Phe and 0.2% Tyr; KMT providing additional 0.62% Lys, 0.22% Met, and 0.61% Thr. All calves were fed the same milk allowance program and were weaned at 56 d of study. Concentrate intake was limited to minimize interference of potential differences in solid feed intake among treatments. Animals were weighed weekly, intakes recorded daily, and blood samples obtained at 2, 5, and 7 wk of study to determine serum urea and plasma AA concentrations. The file presents data of the backwards selection process to assess the model that fitted better ADG with the study variables (performance, intake, plasma AA balances). Data was collected at Torre Marimon IRTA calf facilities (Caldes de Montbui, Spain) during 2017.

The effects on growth performance of supplementation of four different AA combinations in a milk replacer (MR, 25.4% CP and 20.3% fat) based on skimmed milk powder and whey protein concentrate were evaluated in 76 Holstein male calves (3 ± 1.7 d old). The 4 MR were: CTRL with no AA supplementation; PG supplying additional 0.3% Pro and 0.1% Gly; FY supplying additional 0.2% Phe and 0.2% Tyr; KMT providing additional 0.62% Lys, 0.22% Met, and 0.61% Thr. All calves were fed the same milk allowance program and were weaned at 56 d of study. Concentrate intake was limited to minimize interference of potential differences in solid feed intake among treatments. Animals were weighed weekly, intakes recorded daily, and blood samples obtained at 2, 5, and 7 wk of study to determine serum urea and plasma AA concentrations. The file presents data of the backwards selection process to assess the model that fitted better ADG with the study variables (performance, intake, plasma AA balances). Data was collected at Torre Marimon IRTA calf facilities (Caldes de Montbui, Spain) during 2017

The aim of SVGMap is helping in the visualisation of experimental data which are associated with some graphical representation. Thus SVGMap browser allows to generate images with colored areas corresponding to the chosen data and color scale./nThe data is represented as a table and is searchable. All data as well as the generated images/figures can be exported easily through the interface./nAdditionally the tool allows to manage (add, edit or delete) experiments and configure the front-end user search appearance such as the number of images to be displayed, the scale types to use and more.