Search Results for "c:\program files\micronetics\msmws\program\" - Page 3
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Showing 292 open source projects for "c:\program files\micronetics\msmws\program\"
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...PTEROS DEVELOPMENT MOVED TO GITHUB !!! New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
...Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviors recorded at different beamlines. ... -
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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detectMITE
Detection of Miniature Inverted Repeat Transposable Elements
detectMITE - a MATLAB-based tool for detecting miniature inverted repeat transposable elements (MITEs) in genomes. [1] Who are we? Please visit website: http://bioinfolab.miamioh.edu [2] How to cite detectMITE? Ye C, Ji G, Liang C (2016) detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. Sci. Rep. 6, 19688. http://www.nature.com/articles/srep19688 Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation. ... -
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BOWS
Bioinformatics Open Web Services
...If a new process is found, the “arrow” script should change the requisition status from waiting to running, run the process in the HPC cluster and, when the job is complete, call a BOWS back-end service to send the results. The results will then be available to the requestor. BOWS is called from the front-end by Web Services, therefore a program running in a simple computer can benefit of high performance computation executed elsewhere. doi:10.1186/s13104-015-1190-0 -
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MPprimer
a program for reliable multiplex PCR primer design
...These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons of similar electrophoretic mobility. Results: A new program named MPprimer was developed to help users design primer sets for multiplex PCR with high reliability. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. -
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KAPPA (Key Aminoacid Pattern-based Protein Analyzer) is a sequence search program dedicated to the discovery and clustering of proteins defined by a key aminoacid pattern.
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
...MSTgold accepts single-character data that are nucleotides, amino acids, binary characters, or SNPs; integers that represent, for instance, the lengths of VNTRs or microsatellites; and distance matrices. The MSTgold package includes Mac OS X, Linux, and Windows executables of the MSTgold program, a detailed Manual, example data and results, and executables of the program Fasta2MSTG which converts Fasta sequence files to the MSTgold input format. -
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge is... -
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Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel sequences from the search taxon. -
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Saguaro Genome-Wide is a program to detect signatures of selection within populations, strains, or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in the genome.
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Fast Neurite Tracer
Semi-automatic neurite tracing with tera-bytes of imaging data.
Fast Neurite Tracer (FNT) is a tool for semi-automated neurite tracing. FNT can handle big imaging data such as fMOST data. It can also process other types of light imaging data in general. FNT is designed to be * accurate in tracing (each tracing step needs your confirmation), * fast (operations using computer mouse is reduced with automatic searching), * scalable (large volume data of tera-bytes in size are supported). Other features include * the results can be exported to... -
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Kinannote
Protein Kinase Identification and Classification
...If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. Kinannote runs on a unix command line and depends on local hmmer 2 and Blast 2.24 installations. Citing Kinannote: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily Jonathan M. Goldberg; Allison Griggs; Janet L. Smith; Brian Haas; Jennifer Wortman; Qiandong Zeng Bioinformatics 2013; doi: 10.1093/bioinformatics/btt419 http: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full pdf: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full.pdf+html -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
...MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result). The program provide a step praramter (8 steps) which can allow running program from any step and finishing all remaining steps. You also can run step by step using each step program. Please run these step programs at the same directory for running main program MITP.pl. Some steps are optional (read filter, expression, miRNA class and target). ... -
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SwisTrack 4 is a powerful software for tracking robots, humans, animals and objects using a camera or a recorded video as input source. It contains interfaces for USB, FireWire and GigE cameras, as well as AVI files.
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Entrainer is a Java program (JRE 1.8.0_40+ required, available from http://java.sun.com/javase/downloads/index.jsp) which creates binaural beat frequencies with sound, light and animations for the purpose of entraining one's brain waves.
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This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data
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MUMAL2
Multivariate analysis of MS/MS data using ML techniques
Program described in the paper: MUMAL2: Improving sensitivity in shotgun proteomics using cost sensitive artificial neural networks and a threshold selector algorithm, 2016. By Fabio R. Cerqueira; Adilson M. Ricardo; Alcione P. Oliveira; Armin Graber; Christian Baumgartner. -
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PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).
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VCF Explorer
A desktop application for analyzing whole genome VCF files
he decreasing cost high-throughput technologies led to a number of sequencing projects consisting thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyze exome files are not adequate for large VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Efficient memory management of the program and the elimination of preliminary parsing step enable to carry out the analysis at ordinary computers. ... -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are... -
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A tool for extracting and preprocessing spectral count data for label-free quantitative proteomic analysis. This program is designed to be used with the Trans-Proteomic Pipeline (TPP).
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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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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A... -
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BayesRate
Bayesian estimation of diversification rates
BayesRate is a program to estimate speciation and extinction rates from dated phylogenies in a Bayesian framework. The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae).
