Search Results for "learning linux command line"

The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in...

EMC: Enhanced Monte Carlo; A multi-purpose modular and easy extendable solution to molecular and mesoscale simulations

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

Charmol is a cross-platform GUI/command-line based program for making high-quality pictures of molecular structures, nowadays working on Linux, MacOS and Windows. As output, it produces POV-Ray rendered images or files in VRML format. Charmol is capable of making pictures containing: - from small- to large-size molecules - more molecules together (different settings possible) - orbitals using molden and fchk files (GTO functions up to 'h' angular momentum supported) - surfaces...

The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using...

Although many potential applications exist in chemistry and material science, software to allow the general application of de novo structure-based design methods in supramolecular chemistry was non-existent. To address this limitation we created HostDesigner, a code that builds and evaluates millions of molecules in minutes. This command line executable builds 3D molecular structures by covalently connecting user-defined input fragments with pre-computed hydrocarbon fragments from a library...

hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.

bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite

Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.

This software has moved to http://www.poissonboltzmann.org/.

The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.

An open-source software aimed at unsupervised molecular alignment

Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).

Genomecomb is a package for the analysis of complete genome data. It can be used to compare, annotate and especially filter the results of complete genome sequencing.

An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)

Mychem is a chemoinformatics extension for MySQL.

An open-source software to convert SDF files into TINKER XYZ files (and viceversa) with automatic assignment of MMFF94 atom types, bond types and charges

RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.

... to visualize with pymol. For specific non-pdb input/output of 2nd program there are convertation utils also available. Programs are expected to compile in gcc under cygwin or pure linux environment. Scripts to run many copies of program under pbs/torque cluster system are also available.

This space is not maintained anymore. If you want to get the latest updates on fpocket refer to https://github.com/Discngine/fpocket. Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

A collection of tools to transform common biosequence formats (e.g. EMBL, SWISS-PROT, UniProtKB, GenBank and RefSeq) into the fasta sequence format.

A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).

PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models.

Simulator for transmission electron microscope images and tilt series of biological samples.

Smoldyn is a computer program for simulating reactions and diffusion at a mesoscopic size scale. This scale lies between the more traditional microscopic size scale, in which all or most atoms are considered.