Search Results for "console command"
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Showing 47 open source projects for "console command"
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Stop Storing Third-Party Tokens in Your DatabaseRolling your own OAuth token storage can be a security liability. Token Vault securely stores access and refresh tokens from federated providers and handles exchange and renewal automatically. Connected accounts, refresh exchange, and privileged worker flows included.
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relax
Molecular dynamics by NMR data analysis
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... -
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ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering,... -
Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
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Seqs Extractor is a useful tool, and can reduce ambiguities in analyses which uses BLAST command ine, commonly in the next generation sequencing, Transcriptomics, Proteomics, etc and help extract BLASTed sequences and sequences that contains microsatellites. Seqs Extrator also turns the BLAST command line more friendly.
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fas2svg
Visualize genetic code structure from fasta file.
Generate svg file from fasta file. -
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PPIXpress
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal... -
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CompleXChange
differential analysis of combinatorial protein complexes
The increasing wealth of transcriptomic data and current computational tools enable to infer how protein interactomes and complexomes may be assembled in specific samples. With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z. -
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CABBaGe
Classification Algorithm Based on a Bayesian method for Genomics
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Panacea
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes -
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LMAP
Lightweight Multigene Analyses in PAML
Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V and Antunes A (2016) LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics, 17:354. doi: https://doi.org/10.1186/s12859-016-1204-5 -
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HitKeeper is a database application for use in BioInformatics. It deals with "hits" (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools.
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GPU3SNP
Exhaustive search for third order epistatic interactions using CUDA
GPU3SNP is a multi-GPU tool that exhaustively analyzes case-control datasets looking for 3-SNP combinations that present epistatic interaction. It provides a list with the combinations that have higher Mutual Information, which is used as measure for interaction. It is parallelized using CUDA and can exploit several GPUs in the same node/system. -
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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.
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ENLY
Bioinformatic tool to improve draft genome assemblies by closing gaps
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JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included. Legal notice/Impressum: Klaus Meffert An der Struth 25 D-65510 Idstein sourceforge <at> klausmeffert.de
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,... -
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codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE! Check this out...
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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
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vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. Information on this and other projects can be found on: http://www.altmann.eu
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caplib
Correct, translate and analyze combinatorial library sequencing data
Originally developped to handle PacBio CCS data for an AAV capsid library. This program will extract, correct, translate and analyze the sequencng data, starting from the CCS fastq file. -
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WISP
Weighted Implementation of Suboptimal Paths (WISP)
UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path... -
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The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net
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A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
