The article presents information on PathwayStudio Central, a client-server software for visualization and analysis of biological pathways and gene regulation networks for biomedical research labs, biotechnology companies , and pharmaceutical companies. PathwayStudio Central builds pathways from microarray data,...
Furthermore, although pathway analysis software provides detailed images of interactions among molecules, it does not exhibit how pathways interact with one another or with other biological processes under specific conditions. Methods We propose a novel method to standardize descriptions of enriched pathways...
For the open source biological databases, it is common for the biologists and researchers to refer to many databases in order to pursue inference or analysis;though it is one of the most challenging tasks. Biological pathway data integration is aimed to work with repositories of data from a var...
A new service provided by EMBL (EMBL Software File Server) is described that will make free molecular biology software available to anyone with computer network access. MS-DOS, Apple Macintosh and VAX/VMX are supported at the moment. The programs will be delivered by normal electronic mail; con...
PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to descri... Martina,Kutmon,P Martijn,... - 《Plos Computational Biology》 被引量: 147发表: 2015年 ...
protein groups (1,650 in total) were identifiable in each biological replicate, of which ~60% were consistently present in all three replicates (Fig.8cand Supplemental Table1). Functional analysis with the DAVID software package revealed that all major cellular compartments (nucleus, cytoplasm, mem...
Visualization and picking of membrane proteins in cryoET tomogram is often challenging. Here, the authors developed a software MPicker based on membrane flattening to simplify the visualization, picking, and orientation estimation of membrane proteins. ...
Journal of Open Source Software, 6(67), 3756, https://doi.org/10.21105/joss.03756 View the paper at JOSS or view the PDF directly. Maintenance The Pathway Commons Grounding Search Service is an academic project built and maintained by: Bader Lab at the University of Toronto , Sander Lab ...
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and pr
This paradigm is becoming increasingly popular [21, 23, 43, 44] and among others, “backward-causal” features have been introduced recently in Ingenuity Pathway Analysis software [43]. Using RNAi experimental data, Markowetz et al. showed that upstream pathway relationships between unobserved ...