Search Results for "batch%20script%20editor"
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Showing 26 open source projects for "batch%20script%20editor"
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code" button. ... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
... - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us - kabeermuzammil614@gmail.com MzDOCK Development - Available on WindowsOS and Linux ubuntu 22.04 and more - Software Authorship - Muzammil Kabier -
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The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging (http://www.svi.nl/) for parallel batch deconvolutions.
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal... -
Automate contact and company data extractionGenerate leads at scale without building or maintaining scrapers. Use 10,000+ ready-made tools that handle authentication, pagination, and anti-bot protection. Pull data from business directories, social profiles, and public sources, then export to your CRM or database via API. Schedule recurring extractions, enrich existing datasets, and integrate with your workflows.
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'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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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.
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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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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cy2fluxviz
cy2fluxviz : Cytoscape 2 plugin for flux distribution visualization
cy2fluxviz - Cytoscape 2 Plugin for the visualization of flux distributions in networks. Latest releases from https://github.com/matthiaskoenig/cy2fluxviz -
Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
...It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs sequence alignment and deposits sequences into a fasta sequence file for downstream molecular evolutionary analysis. -
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WM Hyperintensities Segmentation Toolbox
Open Source White Matter Hyperintensities Segmentation Toolbox
Wisconsin White Matter Hyperintensity Segmentation [W2MHS] and Quantification Toolbox is an open source MatLab toolbox designed for detecting and quantifying White Matter Hyperintensities (WMH) in Alzheimer’s and aging related neurological disorders. WMHs arise as bright regions on T2- weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer’s disease (AD) with regard to its prognosis. Our toolbox... -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
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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 address when the job is done. (You will need to modify the source code to change the content to meet your special needs) Run-time information will be displayed in a JAVA output window. -
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Dress Up RNA seq
End-to-end automated pipeline of RNA seq packages for an HPC system
...RNA seq programs included are TopHat, CuffLinks, CuffDiff, CuffMerge, FastQC, and trimming using the FastX toolkit. DressUp facilitates RNA seq programs by streamlining various packages into a single script. That script executes the RNA seq programs on a batch cluster system. Upon execution of the script, jobs are submitted to the cluster depending on attributes set up in the configuration file. Program options can be modified in the main script "DressUp", and PBS options can be modified from the HeaderFiles directory. -
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A MATLAB package for wavelet analysis of circadian rhythms with both discrete (Daubechies) and continuous (Morlet) wavelets, as well as tools for batch processing of multiple time series, all accessible through a graphical user interface.
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A batch primer selection program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. BOSS will select oligos for gap closure of both contig and scaffold gaps. See readme for details.
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Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.
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Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.
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A bioinformatics package to analyse ESTs (Expressed Sequence Tags) easily. It contains functionalities of ESTs for EST submission, Batch BLAST and BLAST result parser, etc. easiEST contains JAVA GUI applications for analysing ESTs or other sequences
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Biolet is project aimed to analyze genomic DNA sequences using wavelets. Of additional interest may be a batch processing tool for doing round-robin scheduling of jobs on a beowulf cluster. For that checkout the project robin from the CVS.
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GridSweeper makes it easy to perform batch runs of scientific simulation programs on computational grids/distributed resource management systems.
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X_batch is a plugin for SPM2, which allows the user to create, store, exchange and execute custom batch scripts and record information into a Protege-based ontology.
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What is it:<br> ----------<br> A simulation of a very simplified aunts nest. <br> It is a restricted area (square) fullfill with aunts and rice.<br> Rice is first randomly positionned in the area and aunts will sort it in a unique batch. <br>
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The Java Batch System (JBS) is a batch queueing system in the tradition of NQS and PBS for internal (Java-based) and system batch jobs. Stand-alone operation and integration with existing batch queueing systems, initially OpenPBS, is supported.
