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Showing 139 open source projects for "code"
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AlphaGenome
Programmatic access to the AlphaGenome model
The AlphaGenome API provides access to AlphaGenome, Google DeepMind’s unifying model for deciphering the regulatory code within DNA sequences. This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can deliver predictions at single-base-pair resolution for most outputs. ... -
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iCn3D
Web-based protein structure viewer and analysis tool
...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. View a 3D structure in iCn3D, input a PDB ID, and click "Load". You can also click the "File" menu to "Open File" or input other IDs. You can open a browser in your Virtual Reality (VR) headset and view a 3D structure in iCn3D. Then click the button "Enter VR" at the bottom center of your browser to enter the VR view. ... -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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PUMA Repository
Pascal Units for Medical Applications
The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers. -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
...It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. To contact us, see: https://bioxtas-raw.readthedocs.io/en/latest/help.html -
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CyberUnits
Class library for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. -
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OpenClinic GA
Open Source Integrated Hospital Information Management System
OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities. OpenClinic GA and OpenClinic GMAO are owned by Frank Verbeke, MD, PhD at Post-Factum BV (https://www.post-factum.be) -
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PlateEditor
PlateEditor, a free web application to work with multi-well plates
...It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data. It doesn't require any installation. - PlateEditor is available at this address: https://plateeditor.sourceforge.io - The source code is also available on GitHub, visit: https://github.com/vindelorme/PlateEditor More information about the source code and the API are available there (the wiki is still under construction, thanks for your patience!) For a list of recent updates, visit: https://sourceforge.net/p/plateeditor/wiki/Updates/ Hoping PlateEditor will make your life easier in the lab! ... -
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
...It provides a number of tools for: (a) segmenting z-stacks of fluorescence images; (b) reconstructing the 3D surface of the aggregates and estimating several features (including the volume). ReViMS is written in MATLAB (The MathWorks, Inc., Massachusetts, USA). It is an open-source tool and the source code is freely available at: http://sourceforge.net/p/revims Requirements: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. -
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Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
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UnityMol
Molecular viewer and prototyping framework
!!! New website is https://unity.mol3d.tech and new releases/source code are now on Github : https://github.com/LBT-CNRS/UnityMol-Releases !!!! Implementation of a visualization prototype for molecular structures and networks using the Unity3D game engine. Implementation of numerous graphical methods as spheres, particle systems, bond, etc.. as well as our recent HyperBalls methodology (see: www.hyperballs.sf.net). -
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GenForm
Generation of molecular formulas by high-resolution MS and MS/MS data
...The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can be downloaded here: https://sourceforge.net/p/genform/code/HEAD/tree/trunk/data/ A first program call could look like this: GenForm ms=SinapinicAcidMs.txt msms=SinapinicAcidMsMs.txt exist out -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. -
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The Simplest Manual Counter
Manual counter with the keyboard or the mouse on images
The only open source counter to count any items the simplest and easiest way with the keyboard, or the mouse specifically on images. After associating a key to each item, or a predefined graphical symbol for images, pressing the key or clicking on the image increments its associated counter, and displays (for the images) the symbol at the mouse's pointer location. Such a project is so simple a child could use it! -
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GroIMP
Growth-grammar related Interactive Modelling Platform
Important: Groimp migrates to Gitlab. You can find the latest code at "https://gitlab.com/grogra/groimp/". The version on Sourceforge will not be updated anymore. The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support... -
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Xmaldi
Viewing collections of MALDI spectra and perform PCA and DFA analyses
Xmaldi is an application for viewing collections of MALDI spectra and perform PCA and DFA analyses on them (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/xmaldi3/code/ci/default/tree/README.md -
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CStone
Short-read de novo assembler that identifies chimeric contigs.
> CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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JSONVisor
Visor for mass spectrometry JSON files generated by Integrator
Visor for mass spectrometry JSON files generated by the Integrator program (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/jsonvisor3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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dualword-chem
chemical viewer
chemical viewer written in C++ (Qt, RDKit) Source code: http://github.com/dualword/dualword-chem -
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LaiaMotifs
Search for MHC-like motifs in peptide collections
Search for MHC-like motifs in peptide collections (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/laiamotifs3/code/ci/default/tree/README.md -
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KimBlast
Blast+ the easy way
KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md -
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viRome
R code/package for virus small RNA sequence data
Please use code here: https://github.com/mw55309/viRome_legacy -
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Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
...MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php
