Search Results for "command-line"

This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.

RoadRunner represents a state-of-the-art simulation library for SBML models. It is fast, portable and accurate. This projects hosts the library and tools using the library.

The Systems Biology Results Markup Language is a language describing data. Unlike flat data formats, SBRML allows describing the origin of the data as well. This project hosts a library and tools for using SBRML.

Morpheus is a mass spectrometry–based proteomics database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast—up to nearly 5 times faster than OMSSA for large human datasets. It is written in C# and is available...

Project now hosted at GitHub: https://github.com/djparente/coevol-utils

BLAST (Basic Local Alignment Search Tool) is a popular program that retrieves a library of sequences that resemble the query. The major problem experienced by new users of BLAST revolves around constructing syntactically and semantically correct command line, getting input files into acceptable formats and assessing the output. Visual BLAST is a Graphical User Interface written in C# and it was developed to simplify the parameters setting for BLAST searches. Visual BLAST aims to make BLAST searches accessible to a wider audience with no bioinformatics skill and to facilitate usage among the existing. ...

An assessmemt tool of sequence repeats for short read sequencing.

Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.

"Blue Planet" is a research project simulating the behaviour and darwinian evolution of unicellular lifeforms, each controlled by its own genetic program. Moreover, "Blue Planet Inhabitants" are suited for swarm intelligence and swarm research.