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Perl's second wave of adoption came from the growth of the world wide web. Dynamic web pages—the precursor to modern web applications—were easy to create with Perl and CGI. Thanks to Perl's ubiquity as a language for system...

142.150.188.236 - NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto is a software system for scaleable visualizing and analyzing networks. The current version, NAViGaTOR 3, increases modularity, improves scaleability, extends input/output...

The Brent Lab is developing and applying computational methods for mapping gene regulation networks, modeling them quantitatively, and engineering new behaviors into them.

github.com - The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc...

To remove all line ends (\n) from a Unix text file: sed ':a;N;$!ba;s/\n//g' filename.txt > newfilename_oneline.txt To get average for a column of numbers (here the second column $2): awk '{ sum += $2; n++ } END { if (n > 0) print sum / n;...

bioinformatics.sdstate.edu - 2/3/2020: Now published by Bioinformatics. 11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more. 5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal...

The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the...

advaitabio.com - The confusion about gene ontology and gene ontology analysis can start right from the term itself. There are actually two different entities that are commonly referred to as gene ontology or “GO”: the ontology itself, which is a...

Here is a small tutorial on how to make best use of multiple processors for bioinformatics analysis. One best way is using perl threads and forks. Knowing how these threads and forks work is very important before implementing them. Getting to know...

diytranscriptomics.com - A semester-long course covering best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies, with a primary focus on empowering students to be independent in the use of lightweight and open-source...