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Showing 17 open source projects for "scripts"
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Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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Total Network Visibility for Network Engineers and IT ManagersThis means every device on your network, and every interface on every device is automatically analyzed for performance, errors, QoS, and configuration.
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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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MAF
Bash Framework to combine many preprocessing and alignment tools
DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom... -
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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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OpenGrowth
OpenGrowth is a program which constructs de novo ligands for proteins.
...To use OpenGrowth, you will need OpenGrowth_1.0.zip and Resources_1.0.2.zip that can be found by clicking on the Files menu in the horizontal bar at the top (https://sourceforge.net/projects/opengrowth/files). OpenGrowthGUI, FOG2.0, and the 3Mer-Screen stand-alone can be found in OpenGrowth_1.0.zip. To prepare new fragments you need BuildingFragments_1.0.1.zip and the scripts for MD simulations are in MD-Scripts_1.0.1.zip. SMoG2016.tar.gz allows to compute a score with the newly developed function (J. Chem. Inf. Mod., http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00610). For any questions, please send emails exclusively at opengrowth-discuss@lists.sourceforge.net. -
Free and Open Source HR SoftwareGive your HR team the tools they need to streamline administrative tasks, support employees, and make informed decisions with the OrangeHRM free and open source HR software.
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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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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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. ... -
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PyCancerDB
Cancer Proteomics Database display and management
PyCancerDB is a source code distribution providing a Web-based interface for browsing and updating the Cancer Proteomics Database, together with scripts for maintaining the database. -
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PolySim
Polymer simulation utilites
...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. -
Point of Sale. Powerful and Simple.Vibe Retail is an all-in-one retail point-of-sale and operations platform built for single-store and multi-location retailers seeking to unify inventory, sales, staff and customer data from one mobile-friendly interface. The system lets you track inventory across locations and warehouses, handle item variations (size, color, material), manage purchase orders and supplier deliveries, print custom barcodes, and transfer stock between stores in real time. On the sales side, Vibe supports multiple payment types (cards, cash, checks, gift cards, EBT), layaway workflows, serial number tracking, delivery management, loyalty programs and branded receipts. Retailers can integrate with online platforms (such as Shopify and WooCommerce), sync in-store and online sales, access 40+ real-time reports on sales, inventory and performance, set up promotions and discounts, and print receipts from mobile devices.
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
...The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code. -
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...Have a look at the readme file when you download your new copy from https://sourceforge.net/projects/rawgeno/files/rawgeno/RawGeno%202.0-1/ Make also sure to have a look at https://sourceforge.net/projects/rawgeno/files/ where you can find a detailed manual, demo datasets and many demo scripts.
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NaRIBaS
Unix-based preparation and analysis toolbox for molecular simulations
Unix-based preparation and analysis toolbox for Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab using bash scripts, Gromacs tools and Matlab functions. NaRIBaS provides a framework that decouples user input parameter and terminal based command lines. NaRIBaS does not replace a simulation software and specific analysis tools like Gromacs, but it allows iterative repetition of tasks while changing specific input parameter. The toolbox is to be understood as a scripting framework rather than a black-box software. ... -
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u/sbmv2012
Taxonomy assignment of metazoans using a python based pipeline
The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples. We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database. -
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This is a set of scripts that helps with processing of NMR pH titration data. These scripts allow for fitting (using R) and plotting of data of multiple residues. The program needs to be made more user friendly.
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Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.
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A repository of Python extension scripts for use with the Sparky (http://www.cgl.ucsf.edu/home/sparky) NMR assignment package. No packaged releases yet, but there are scripts in the Sourceforge CVS@ http://sparkyscripts.cvs.sourceforge.net/sparkyscripts
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