Search Results for "learning linux command line"
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18 programs for "learning linux command line" with 2 filters applied:
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Our robust pre-built connectors and our no-code, drag-and-drop interface makes it easy and fast to automatically sync vendors, invoices, and invoice payment data between Tipalti and your ERP or accounting software.
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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Crux-Toolkit
Software toolkit for tandem mass spectrometry analysis
Crux is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. If you use Crux in your research, please cite Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022--3027, 2008. -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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MCCCS
Multi Channel Classification and Clustering
Here we present an image-based Multi Channel Classification and Clustering System (MCCCS). It is an generalized, script-based classification system for processing various kinds of image data. Due to the modular design, individual processing-components can be easily adapted, extended or exchanged by own extensions. See project website for installation instructions. -
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ENLY
Bioinformatic tool to improve draft genome assemblies by closing gaps
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BIRAP
Bacterial Intergenic Region Analysis Pipeline
BIRAP (Bacterial Intergenic Region Analysis Pipeline) is an open source, easy to use Perl pipeline that can be used to re-annotate bacterial genomes using experimental data. The tool integrates expression profile derived from RNA-seq and/or proteogenomics, compares it with existing in silico annotation and helps validate annotation, identify novel protein coding regions, putative non-coding RNA as well as help correct er-rors in the existing annotation. The pipeline requires “pileup” output... -
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Description: PseAAC-Builder is a cross-platform stand-alone program for generating protein pseudo-amino acid compositions. This is a bioinformatics program. It performs faster than the existing PseAAC server. Reference: [1] Pufeng Du, Shuwang Gu, Yasen Jiao. PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets. International Journal of Molecular Sciences 15 (2014) pp.3495-3506 [2] Pufeng Du, Xin Wang,...
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Seqshell
A JAVA GUI for performing the function of Tophat and Cuffdiff
Combines the Tophat and Cuffdiff functions in one GUI interface. tophat and cuffdiff are required to be pre-installed in the system. By modifying the program, it can be used to execute any command line programs even R packages since R can also be run from commandlines. New functions: Batch processing function for Tophat. You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email... -
ConnectWise ScreenConnect, formerly ConnectWise Control, is a remote support solution for Managed Service Providers (MSP), Value Added Resellers (VAR), internal IT teams, and managed security providers. Fast, reliable, secure, and simple to use, ConnectWise ScreenConnect helps businesses solve their customers' issues faster from any location. The platform features remote support, remote access, remote meeting, customization, and integrations with leading business tools.
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DeNovoCheck
DeNovoCheck: Inheritance analysis for NGS trio data
DeNovoCheck is intended to be used for inheritance analysis in NGS tio data. For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants. -
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BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.
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HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
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EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
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Neurofitter is a parameter tuning package for electrophysiological neuron models. For more information please take a look at http://neurofitter.sourceforge.net
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SaskSAGE is package designed to exploit SAGE data. Csage is employed to identify and match SAGE tags in a biologically meaningful manner. Tags are analyzed for significance using a Chi squared test for independence between TAG and treatment.
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This is a collection of softwares that I have been using in my research on protein interaction network. By release them under the GPL 2.0 lience, I hope that they can be useful to others, as well.
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biojazz
In silico evolution of biochemical networks.
In silico evolution of biochemical networks using a genetic algorithm combined with a rule-based biochemical network model. -
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gene2path
A tool to study fish gene pathways by search of orthologous genes
Most of the gene regulation pathways data from experiments are drawn from humans or from species commonly used as experimental animal models. Accordingly, the software packages to analyse these data on the basis of specific gene identification codes (IDs) or accession numbers (AN) are not easy to apply to other organisms that are less characterized at the genomic level. Here, we have developed the Gene2Path programme which automatically searches pathway databases to analyse microarray...
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