Search Results for "user mode linux" - Page 8
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Showing 268 open source projects for "user mode linux"
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This is an implementation of the adaptive biasing force method (ABF) in NAMD. The code for ABF was developed by Eric Darve, Stanford University. ABF is a method created by E. Darve and A. Pohorille to calculate the free energy of bio-molecules.
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LabDiary is a program for managing laboratory experiments in a sophisticated way. It is very easy to use - you can link experiments logically with each other, associate files to an experiment and structure all your data.
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LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal. !!!!!! PROJECT MOVED TO GITHUB !!!!!! Please check out http://raphaelbauer.github.io/lajolla/
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CellMC is a multi-platform XSLT-based SBML compiler producing executable SSA models based on the optimised direct method.
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NMkit is used in vibrational Normal Mode analysis. Using Gaussian Software's output, it determines the internal coordinate representations of normal modes, and performs other geometric manipulations in Internal Coordinate space.
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SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
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Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.
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Sudsy is a saponification calculator coded in Python. The CLI works fine, but the PyGTK version still needs some work...The interface is designed and it starts up, but some of the callbacks still need to be implemented. Let me know if you can help.
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Goldify is a set of tools that allow automated addition of links into electronic documents. Its main purpose is to allow such addition of links into documents that wish to link to the IUPAC GoldBook (http://goldbook.iupac.org).
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Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.
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PyChemEq is an Open Source project which goal is to simulate chemical equilibrums. It provides classes (that are the project's "kernel" ) and a user interface using PyGtk and Glade. The whole project will be written in Python.
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The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.
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RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.
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JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
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ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
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Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/
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WebBabel is a python web application using OpenBabel to convert files from one format to another. It runs under Windows, Mac or Linux on your desktop, workstation or laptop. It uses the Jmol (or Marvin) viewer to show the structures being converted.
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Command line molar mass calculator that provides typo checking and options for printing elemental analysis and saving a record of previously calculated molar masses.
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User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files
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FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.
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Oscilib (Open Science Library) aims to be a comprehensive suite of programs that provide a simple useful way to solve common scientific and mathematical problems.
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This is the first force-matching software published with the ability to do general coarse-graining for molecular systems.
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BINViz(Bidirectional Interactive Network Visualization) is a JavaScript library for network and graph visualization. The goal of this tool is to provide a better way to visualize complex graphical models and the underlying data in a web-based environ
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A tool to convert mol or sdf files to SVG - scalable vector graphics. Sdf and mol files are files containing information about chemicals. The tool is written in PHP.
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The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.