label
description
image
logo image
copyright license
software version identifier
depends on software
developer
file extension
platform
programmed in
operating system
media type
user manual URL
issue tracker URL
official website
readable file format
writable file format
.NET Bio
Microsoft free software
1000minds
Online decision-making and conjoint analysis software company
https://www.1000minds.com
3D Virtual Creature Evolution
evolution simulation program
https://3dvce.fandom.com/wiki/Main_Page
A.nnotate
web service for storing and annotating documents
http://a.nnotate.com/
Portable Document Format
AIMAll
quantum chemistry software package
proprietary license
Microsoft Windows macOS Linux
http://aim.tkgristmill.com/index.html
Portable Network Graphics TIFF JPEG File Interchange Format (JFIF) Windows Bitmap Portable Document Format
ALEGRA
software
Sandia National Laboratories
http://www.cs.sandia.gov/ALEGRA/Alegra_Home.html
ALGOR
finite element analysis software
Linux
Algor FEMPRO model
Algor FEMPRO model
ASReml
software for Microsoft Windows and Linux
Microsoft Windows Linux
https://www.vsni.co.uk/software/asreml/
ASTOS
software for Microsoft Windows and Linux , from 1989
Microsoft Windows Linux
http://www.astos.de http://www.astos.de/products/astos
ATLAS.ti
computer program
proprietary license
Thomas Muhr
Microsoft Windows macOS Android
http://atlasti.com/manuals-docs/
http://www.atlasti.com/
Abalone
molecular dynamics and molecular graphics computer program
proprietary license
http://www.biomolecular-modeling.com/Abalone/Manual.html
http://www.biomolecular-modeling.com/Abalone/
HyperChem Input File SYBYL line notation Protein Data Bank XYZ file format MLM
HyperChem Input File Protein Data Bank XYZ file format MLM
Accelerator Physics Codes
software
Affymetrix GeneChip Operating Software
software system for managing Affymetrix microarray data
Affymetrix
https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html
Agfa impax 6
PACS client for Windows-based PCs
Agfa-Gevaert
AlleleID
desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification
Microsoft Windows macOS
http://www.premierbiosoft.com/bacterial-identification/index.html
FASTA format GenBank file format
Amira
software platform for 3D and 4D data visualization
Zuse Institute Berlin Thermo Fisher Scientific Inc.
Windows XP
https://www.fei.com/software/amira-user-guide/
https://www.fei.com/software/amira-avizo/ http://www.amira.com
Windows Bitmap Drawing Interchange File Format Family HTML Digital Imaging and Communications in Medicine file Protein Data Bank Virtual Reality Modeling Language Polygon File Format AmiraMesh ASCII file format AmiraMesh 3D ASCII 2.0 file format AmiraMesh 3D Binary 2.0 file format AmiraMesh 3D Binary Little Endian 2.0 file format AmiraMesh Binary Little Endian 2.1 file format
Encapsulated PostScript Windows Bitmap Drawing Interchange File Format Family Wavefront .obj file Virtual Reality Modeling Language Polygon File Format AmiraMesh ASCII file format AmiraMesh 3D ASCII 2.0 file format AmiraMesh 3D Binary 2.0 file format AmiraMesh 3D Binary Little Endian 2.0 file format AmiraMesh Binary Little Endian 2.1 file format
AnimatLab
neuromechanical simulation software
C++
http://animatlab.com
AnyLogic
multimethod simulation modeling tool
7.1.2
Java Virtual Machine
Java
cross-platform
https://www.anylogic.com/
AnyLogic Project
AnyLogic Project
Aphelion
image processing and analysis software suite
4.4.0
C#
Microsoft Windows
http://www.adcis.net/en/Download/Help-Files.html
http://www.adcis.net/en/Products http://www.adcis.net/en/Products/Aphelion-Imaging-Software-Suite.html
Application Mapper
multiple sequence alignment software program
http://bio.math.berkeley.edu/amap/download/
FASTA format
FASTA format Clustal file format
Aqion
hydrochemistry software tool
freeware
6.1.0
C++
Microsoft Windows
http://www.aqion.de/site/98
http://www.aqion.de
Archaeopteryx
software for viewing, editing, and analyzing phylogenetic trees
0.9917
Java
Microsoft Windows Linux macOS
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx https://sites.google.com/site/cmzmasek/home/software/forester
PhyloXML Nexus file
Nexus file PhyloXML
Archim
freeware program for making graphs in two or three dimensions
freeware
http://www.stochastic-lab.com:80/archim.html
Arlequin
population genetics software
3.5.2.2
SIB Swiss Institute of Bioinformatics
http://popgen.unibe.ch/software/arlequin35/man/Arlequin35.pdf
http://cmpg.unibe.ch/software/arlequin3/
ArrayTrack
multi-purpose bioinformatics software tool
1.0.0
Food and Drug Administration
https://www.fda.gov/downloads/ScienceResearch/BioinformaticsTools/Arraytrack/UCM250045.pdf
http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Atomistix ToolKit
software for atomic-scale modeling and simulation of nanosystems
Atomistix
http://docs.quantumwise.com/manuals/manual.html
http://www.quantumwise.com/
netCDF
netCDF
Atomistix Virtual NanoLab
software
Auto-Latex Equations
Google Docs add-on for LaTeX equations
https://sites.google.com/site/autolatexequations/home
Autochem
automatic code generator and documentor for atmospheric chemistry modeling
David Lary
Fortran 90
http://www.science-softcon.de/autochem/index.html
Autodesk Ecotect Analysis
environmental analysis tool that allows designers to simulate building performance
Autodesk
Automated Anatomical Labeling
software package and digital atlas of the human brain
MATLAB SPM
MATLAB
http://www.cyceron.fr/index.php/en/plateforme-en/freeware https://www.gin.cnrs.fr/en/tools/aal/
Automated Data Inquiry for Oil Spills
software model for oil weathering
National Oceanic and Atmospheric Administration
Microsoft Windows macOS
http://response.restoration.noaa.gov/oil-and-chemical-spills/oil-spills/response-tools/downloading-installing-and-running-adios.html
Avizo
software for scientific and industrial data visualization and analysis
http://www.vsg3d.com
BAli-Phy
software
http://www.bali-phy.org/
BLAT
pairwise sequence alignment algorithm
Jim Kent
https://genome.ucsc.edu/goldenPath/help/blatSpec.html
http://genome.ucsc.edu
BNAber
integrated web resource focused on maintaining a comprehensive database of broadly neutralizing HIV-1 antibodies
Sanford Burnham Prebys Medical Discovery Institute
http://www.bnaber.org/
Baudline
software
FreeBSD Linux Solaris macOS
http://www.baudline.com
Beacon designer
software for the design of primers and probes for real time PCR assays
Premier Biosoft
http://www.premierbiosoft.com/molecular_beacons/index.html
GenBank file format FASTA format SNP file format
GenBank file format FASTA format SNP file format tab-separated values
Bellerophon
software for detecting chimeric sequences in multiple sequence datasets
http://comp-bio.anu.edu.au/bellerophon/bellerophon.pl
Sequence Alignment/Map
Bilbao Crystallographic Server
website offering online crystallographic database and programs
http://www.cryst.ehu.es
Bing Maps Platform
geospatial mapping platform by Microsoft
Microsoft
Microsoft Windows
http://www.microsoft.com/maps/
BioBIKE
cloud-based bioinformatics platform
MIT License
Common Lisp
http://www.biobike.org http://biobike.csbc.vcu.edu/
BioExtract
bioinformatics software
http://bioservices.usd.edu/bioextract/help/BioExtractServerUserManual.pdf
https://www.bioextract.org/query/index.jsp
FASTA format
BioLinux
projects involved in bioinformatics software on Linux
BioModels Database
database of biological reactions
Creative Commons CC0 License
European Bioinformatics Institute Babraham Institute California Institute of Technology
http://www.ebi.ac.uk/biomodels-main/ https://www.ebi.ac.uk/biomodels-main/
BioNumerics
bioinformatics software suite
Applied Maths
Microsoft Windows
http://www.applied-maths.com
BioPHP
software
PHP
http://biophp.org/
BioPerl
collection of Perl modules for bioinformatics
Artistic License
1.7.7
Perl
https://bioperl.org
Bioconductor
software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology
Artistic License
3.6
R
Linux macOS Microsoft Windows
http://www.bioconductor.org/
FASTA format
Bioinformatic Harvester
defunct bioinformatic meta search engine
http://harvester.kit.edu
Blast2GO
bioinformatics platform for high-quality functional annotation and analysis of genomic datasets
BioBam Bioinformatics
Java
http://www.blast2go.de
Budapest Reference Connectome
parametrizable consensus brain graph
Perl
http://pitgroup.org/connectome/
CADEC
software application that performs composite materials analysis
http://help.cadec-online.com/UserManualEN/
http://cadec-online.com
CARET
neuroimaging software
http://brainvis.wustl.edu/
NII
CASINO
quantum Monte Carlo program
Theory of Condensed Matter group
http://www.tcm.phy.cam.ac.uk/~mdt26/casino_manual_dir/casino_manual.pdf
https://vallico.net/casinoqmc/
CASTEP
density functional theory software
Theory of Condensed Matter group
Fortran
http://www.castep.org/
CASTp
software
http://sts-fw.bioengr.uic.edu/castp/index.php
Protein Data Bank
CFD-ACE+
commercial computational fluid dynamics solver
ESI Group
CFD-FASTRAN
Computational Fluid Dynamics software package
ESI Group
https://www.esi-group.com/software-solutions/virtual-environment/cfd-multiphysics/ace-suite/cfd-fastran
CIP-Tool
software tool for the modeling and implementation of event-driven applications
ETH Zurich
http://www.actifsource.com/solutions/cip_tool/
COGO
suite of programs used in civil engineering
https://www.cogosoftware.com/
COLUMBUS
computational chemistry software suite
CONQUEST
linear scaling, or O(N), density functional theory (DFT) electronic structure code for modelling atom structures
CORSIKA
physics software
https://web.ikp.kit.edu/corsika/usersguide/usersguide.pdf
https://www.ikp.kit.edu/corsika/
COmputer STored Ambulatory Record
software for electronic medical records
Massachusetts General Hospital
CPCe
scientific software
CS23D
web server to generate 3D structural models from NMR chemical shifts
University of Alberta
http://www.cs23d.ca/index.php
Cambridge Algebra System
computer algebra system
Stephen R. Bourne John Fitch
ALGOL 68C BCPL
Cartopedia
atlas computer program
Car–Parrinello molecular dynamics
computational chemistry software package
ChemDraw
software for chemical structure drawing
PerkinElmer
macOS Microsoft Windows iOS
https://www.cambridgesoft.com/
CDX Format CDXML MDL Molfile Structure-data file ChemDraw file Chem3D model ChemDraw Template
ChemDraw file ChemDraw Template
ChemWindow
chemical structure drawing and publishing program
Bio-Rad Laboratories
http://www.bio-rad.com/en-us/product/chemical-structure-drawing-software?pcp_loc=catprod
CDX Format MDL Molfile
Chemical WorkBench
software
Citavi
software for reference management and knowledge organization
proprietary license
6.18.0.1
Swiss Academic Software
Microsoft Windows Windows 10 Windows 8.1 Windows 8 Windows 7 Windows Server 2016 Windows Server 2012 Windows Server 2008
http://www.citavi.com
Cleverbot
web application
Rollo Carpenter
http://www.cleverbot.com/
Clone manager
bioinformatics software
http://www.scied.com/pr_cmpro.htm
CloudSim
cloud computing simulator
Java
http://www.cloudbus.org/cloudsim/
CoNTub
software for generating 3D structures of arbitrary carbon nanotube connections
freeware
Java Virtual Machine
Java
http://www.ugr.es/local/gmdm/contub.htm
Code V
software for the design and analysis of optical imaging and optical communication systems
proprietary license
Synopsys
https://optics.synopsys.com/codev/
CodonCode Aligner
software for DNA sequence assembly, sequence alignment, and editing
proprietary license
macOS Microsoft Windows
http://www.codoncode.com/aligner
AB1 file format SCF FASTA format FASTQ format GenBank file format EMBL file format
SCF FASTA format FASTQ format Nexus file PHYLIP file format
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis
cloud computing service
http://www.camera.calit2.net/
Community Earth System Model
numerical simulation of Earth systems
National Center for Atmospheric Research
https://www.cesm.ucar.edu/
CompHEP
software package for automatic computations in High Energy Physics
non-commercial activity
4.5.2rc
SINP MSU
https://theory.sinp.msu.ru/dokuwiki/lib/exe/fetch.php/comphep/manual-3.3.pdf
http://comphep.sinp.msu.ru/
CompuCell3D
C++ software problem solving environment for simulations of biocomplexity problems
4.6.0
C++
http://www.compucell3d.org/Manuals
http://www.compucell3d.org/
Computational Resource for Drug Discovery
computational resources for drug design
Consed
program for viewing, editing, and finishing DNA sequence assemblies
David Gordon
C++
Linux macOS
http://bozeman.mbt.washington.edu/consed/consed.html
CricketGraph
legacy graphics software for Apple Macintosh
Mac
Crucible
geodemography computer system created by the United Kingdom-based grocery company Tesco
DAVID
online bioinformatics resource
freeware
https://david.ncifcrf.gov/content.jsp?file=functional_annotation.html
http://david.abcc.ncifcrf.gov/home.jsp
DISLIN
software
C FORTRAN 77 Fortran 90
Microsoft Windows Linux Unix OpenVMS MS-DOS macOS
http://www.mps.mpg.de/dislin/online-manual
http://www.dislin.de/
DMol3
software package used to calculate the electronic properties of molecules, clusters, surfaces and crystalline solid materials
DP code
software package for physics
http://www.dp-code.org/
DXplain
clinical decision support system
Massachusetts General Hospital
http://www.mghlcs.org/projects/dxplain
Dalton
ab initio quantum chemistry computer program
http://daltonprogram.org/www/resources/dalton2016manual.pdf
https://daltonprogram.org/
Dashboard of Sustainability
software package configured to convey the complex relationships among economic, social, and environmental issues
DataDetective
data mining platform
Sentient Information Systems
DataScene
software for graphing, animation, data analysis, and real-time data monitoring
GNU/Linux Microsoft Windows Unix
http://www.cyber-wit.com/
Datacopia
software for making charts and infographics
http://www.datacopia.com/
comma-separated values tab-separated values text file
Dataplot
software system for scientific visualization, statistical analysis, and non-linear modeling
National Institute of Standards and Technology
Fortran
GNU/Linux Unix macOS Microsoft Windows
http://www.itl.nist.gov/div898/software/dataplot/refman1/homepage.htm
http://www.itl.nist.gov/div898/software/dataplot/index.htm
Deep-Sky Planner
software for Microsoft Windows
Microsoft Windows
Delaunay tessellation field estimator
software
Desmos
browser-based graphing calculator
Desmos
https://www.desmos.com/
DialogOS
graphical programming environment for dialog design
http://www.clt-st.de/produkte-losungen/dialogos/
Dialogue-Assisted Visual Environment for Geoinformation
gesture and voice interface for GIS
Pennsylvania State University
Diffpack
programming environment for developing simulation software
Hans Petter Langtangen
C++ Python Perl
Microsoft Windows GNU/Linux macOS Unix
http://www.diffpack.com/diffpack_reference/
http://www.diffpack.com
Dipmeter Advisor
expert system for oil exploration data
Schlumberger
Interlisp
Dirac
ab initio quantum chemistry program
GNU/Linux Unix macOS Microsoft Windows
http://www.diracprogram.org/doc/release-16/
http://www.diracprogram.org/doku.php
XYZ file format
Discovery Studio
molecular modeling software
BIOVIA
SUSE Linux Enterprise Server
http://accelrys.com/products/collaborative-science/biovia-discovery-studio/
Protein Data Bank Chemical table file MDL Molfile
Distributed Oceanographic Data Systems
software
National Oceanic and Atmospheric Administration
https://dods.ndbc.noaa.gov/
DoctorBase
business and software in United States of America , from 2010
http://www.doctorbase.com
Dr. Sbaitso
artificial intelligence speech synthesis program
Creative Technology
DOS
DrawMD
patient education software
http://www.drawmd.com/
Drug Design and Optimization Lab
distributed computing project for discovering drug candidates
Drugfire
multimedia database imaging system
ECLIPSE
oil and gas reservoir simulator
Schlumberger
https://www.software.slb.com/products/eclipse
EGS
software for simulating radiation therapy sources
SLAC National Accelerator Laboratory
ESMF
earth science software
https://www.earthsystemcog.org/projects/esmf/
ESTAR
software for robotic telescopes
University of Exeter Liverpool John Moores University
ETAP-3
linguistic processing system
http://cl.iitp.ru/etap
EXMARaLDA
free software tools for creating, managing and analyzing spoken language corpora
GNU General Public License
Java
Microsoft Windows
http://www.exmaralda.org/pdf/Partitur-Editor_Manual.pdf
http://www.exmaralda.org/en_index.html
Earth Simulator
highly parallel vector supercomputer system for running global climate models
NEC
http://www.jamstec.go.jp/es/en
Earth System Grid
data distribution portal
EarthBrowser
virtual globe software
Eccky
life simulation game
Ecodrive
automotive software
Microsoft Fiat
http://ecodrive.driveuconnect.eu/
EcosimPro
simulation tool for modelling simple and complex physical processes
Microsoft Windows
http://www.ecosimpro.com
EditGrid
Web 2.0 spreadsheet service
Team and Concepts
http://www.editgrid.com/
Empire
computer program
EnABLE software
history matching and uncertainty assessment software for the oil and gas industry
http://www.emerson.com/en-us/automation/roxar
Engineering Equation Solver
general equation-solving program
http://www.fchart.com/ees/
Enterprise Dynamics
software
proprietary license
Delphi C++
Microsoft Windows
http://www.incontrolsim.com/product/enterprise-dynamics/
Epi Map
mapping module for Epi Info
Centers for Disease Control and Prevention
Visual Basic
Microsoft Windows
https://www.cdc.gov/EpiInfo/
Eurisko
lisp based discovery system written by Douglas Lenat
Douglas B. Lenat
Extensible Computational Chemistry Environment
problem-solving environment for computational chemistry
Pacific Northwest National Laboratory
Linux
https://ecce.emsl.pnl.gov/
FDMNES
physics software
http://neel.cnrs.fr/spip.php?rubrique1007&lang=fr
FEFF
physics software
Fortran
http://monalisa.phys.washington.edu/feffproject-feff.html
FLUKA
monte carlo simulation software
proprietary license
2021.2.1
Istituto Nazionale di Fisica Nucleare
Fortran
Linux
http://www.fluka.org/content/manuals/FM.pdf
http://www.fluka.org/
FORDISC
software for forensic anthropology
http://fac.utk.edu/fordisc-3-1-personal-computer-forensic-discriminant-functions/
FastPCR
software tool for the design of PCR primers and probes
http://primerdigital.com/fastpcr/m1.html
http://primerdigital.com/fastpcr.html
text file Rich Text Format FASTA format
FitIt
software to fit spectra using multidimensional interpolation approximation
http://www.nano.sfedu.ru/research/projects/fitit/
FlexPro
software package for analysis and presentation of scientific and technical data
proprietary license
11.0.8
http://www.weisang.com/
netCDF ASAM MDF Compound File Binary File Format comma-separated values Common Data Format Hierarchical Data Format binary file HTML Waveform Audio File Format
Compound File Binary File Format comma-separated values Common Data Format
Flexpde
partial differential equations software
http://www.pdesolutions.com/help/index.html
http://www.pdesolutions.com/
Drawing Interchange File Format Family Wavefront .obj file
Flood Modeller
software that simulates the flow of water through river channels and across floodplains
CH2M Hill
C#
http://help.floodmodeller.com/floodmodeller/
https://www.floodmodeller.com
FlowJo
software package for analyzing flow cytometry data
FlowJo LLC
https://www.flowjo.com/
FlowJo PC Workspace FlowJo Mac Workspace
FlyExpress
database that collects the expression patterns of Drosophila melanogaster in embryogenesis
freeware
Biodesign Institute
http://www.flyexpress.net
FoldX
protein design software
http://foldxsuite.crg.eu/documentation#manual
http://foldxsuite.crg.eu/
Framsticks
software for simulation of artificial life
http://www.framsticks.com/files/common/Framsticks_Manual.pdf
http://www.framsticks.com/
FreeFem++
Programming and software language
GNU Lesser General Public License
Pierre and Marie Curie University Frédéric Hecht Pierre Jolivet
C++
Linux
http://www.freefem.org
Fusionviewer
medical image display software package
http://fusionviewer.sourceforge.net/docs/FusionViewerUsersGuide.pdf
Portable Network Graphics TIFF JPEG File Interchange Format (JFIF) Windows Bitmap Digital Imaging and Communications in Medicine file
GENSCAN
software program to identify complete gene structures in genomic DNA
Christopher Burge
http://genes.mit.edu/GENSCANinfo.html
GESS
software for analyzing gene expression data obtained from microarrays
http://www.ncss.com/
GEUP
geometry software for interactive math visualization
Windows 10 Windows 8.1 Windows 8 Windows 7 Windows Vista Windows XP Windows 2000 Windows NT 4.0 Windows Me Windows 98 Windows 95
http://www.geup.net/geup7_quickguide.pdf
http://www.geup.net/
GMS
software for building and simulating groundwater models
Aquaveo
http://aquaveo.com/software/gms-groundwater-modeling-system-introduction
ADRG General Information File ARC Standard Raster Product Band Interleaved by Line Image File BigTIFF Compressed ARC Digitized Raster Graphics ERDAS Imagine IMG GRIB GeoPDF JP2 MrSID National Imagery Transmission Format Standard Keyhole Markup Language Zipped PCX file format family Portable Graymap, text variant Portable Network Graphics GeoTIFF Digital orthophoto quadrangle Digital raster graphic MapInfo Interchange Format ZoomifyImageFormat LAS file format dBASE Table File Format Family E57 Lidar Point Cloud Format SOSI
GPOPS-II
software for macOS
macOS
http://gpops2.com
GRAPE
software for for mathematical visualization
University of Freiburg University of Bonn
https://archive.ins.uni-bonn.de/numod.ins.uni-bonn.de/grape/MANUAL/manual/manual.html
http://numod.ins.uni-bonn.de/grape/
GSI3D
software
GYRO
Physics software
General Atomics
https://fusion.gat.com/theory/Gyrogeometry
https://fusion.gat.com/theory/Gyro
Gene Designer
software for gene design
freeware
Microsoft Windows
http://www.dna20.com/resources/genedesigner
GeneMark
gene prediction software
Georgia Tech
Linux macOS
http://opal.biology.gatech.edu/GeneMark/
GenePattern
genomic data analysis software
Broad Institute
http://software.broadinstitute.org/cancer/software/genepattern/user-guide
http://www.genepattern.org
GenePattern GCT format
GenePattern GCT format
Geomodeller3D
software tool for 3D geologic modelling
http://www.geomodeller.com/
Geworkbench
open-source software platform for integrated genomic data analysis
open-source license
Columbia University
Java
Microsoft Windows
http://www.geworkbench.org
Affymetrix File Format Family FASTA format Protein Data Bank
GoTo
type of telescope mount and related software
GoldSim
software for Microsoft Windows
Microsoft Windows
http://www.goldsim.com
Google Sky
Feature for Google Earth and an online sky/outer space viewer at www.google.com/sky
https://www.google.com/sky
Goupile
electronical Case Report Form (eCRF)
GNU Affero General Public License, version 3.0 or later
C++
https://goupile.fr
GraphPad InStat
statistical analysis software
GraphPad Software
Microsoft Windows macOS
http://www.graphpad.com/instat
GraphPad InStat data (Windows)
Windows Metafile PICT GraphPad InStat data (Windows)
GraphPad Prism
2D graphing and statistics software
GraphPad Software
macOS Microsoft Windows
http://www.graphpad.com/guides/prism/7/user-guide/
http://www.graphpad.com/ http://www.graphpad.com/prism
GraphPad Prism file format GraphPad Prism file format, version 4 GraphPad Prism XML document
GraphPad Prism file format GraphPad Prism file format, version 4 GraphPad Prism XML document
Grapher
graphing calculator software
Apple
Encapsulated PostScript Portable Document Format QuickTime File Format
Graphmatica
equation plotter with numerical and calculus features
macOS Microsoft Windows iOS
http://www.graphmatica.com/
HAZUS
software tool for natural hazard analysis
Federal Emergency Management Agency
Windows 10 Windows 8.1 Windows 7
https://www.fema.gov/hazus/
HDF Explorer
data visualization program
Microsoft Windows
http://www.space-research.org/
Hierarchical Data Format netCDF
HEC-RAS
software for modeling the hydraulics of water flow
freeware
4.1
United States Army Corps of Engineers
Windows XP Windows Vista Windows 7 Windows 8 Windows 8.1 Windows 10
http://www.hec.usace.army.mil/software/hec-ras/documentation/HEC-RAS%205.0%20Users%20Manual.pdf
http://www.hec.usace.army.mil/software/hec-ras
HEC-RAS Flow file HEC-RAS Geometry file
HEC-RAS Flow file HEC-RAS Geometry file
HNSKY
night sky simulator software
freeware
Microsoft Windows GNU/Linux
http://www.hnsky.org/help/uk/hnsky.htm
http://www.hnsky.org/software.htm
HNSKY Deep Sky Database
HNSKY Deep Sky Database
HTK
Hidden Markov Model software
proprietary license
Cambridge University Engineering Department
GNU/Linux Microsoft Windows macOS
http://htk.eng.cam.ac.uk/
HYPHY
computational phylogenetics software
http://www.hyphy.org/
HemoSpat
bloodstain pattern analysis software
C++
macOS Windows 7 Windows 8 Windows 8.1 Windows 10
http://hemospat.com
comma-separated values Digital Asset Exchange Drawing Interchange File Format Family Wavefront .obj file Virtual Reality Modeling Language
HipNav
computer-assisted surgery system
Carnegie Mellon University
Huygens Suite
image processing software tools
https://svi.nl/HomePage
I-TASSER
software for for protein structure prediction and refinement, and structure-based protein function annotations
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
IRAP RMS Suite
reservoir characterization and modeling software
Roxar AS
Linux
http://www.roxarsoftware.com http://www.emerson.com/en-us/automation/operations-business-management/reservoir-management-software
ISIS/Draw
chemical structure drawing software for Windows
MDL Information Systems
http://accelrys.com/products/informatics/cheminformatics/draw/index.html
Illyria
software
Common Lisp
Image Studio Lite
software for Western blot analysis
LI-COR Biosciences
Java
macOS Sierra Windows 10
http://www.licor.com/bio/products/software/image_studio_lite/
JPEG File Interchange Format (JFIF) Portable Network Graphics TIFF
Integrated Ballistics Identification System
software for firearm identification
Integrated Software for Imagers and Spectrometers
digital image processing software
United States Geological Survey
C++
Ubuntu Red Hat Enterprise Linux Debian Fedora Linux macOS
https://isis.astrogeology.usgs.gov/Application/index.html
http://isis.astrogeology.usgs.gov
Intel Array Visualizer
software
Polygon File Format
Intelligent Speech Analyser
Finnish speech and voice analyser
Mac OS operating systems
https://www.pitchsys.fi/copyright_protected_ISA_site/Works.html
JME Molecule Editor
molecule editor Java applet
Comenius University
Java
http://www.molinspiration.com/jme
simplified molecular input line entry specification
JUICE
software for editing and analyses of phytosociological data
Masaryk University
http://www.sci.muni.cz/botany/juice/
Jalview
software for multiple sequence alignment editing, visualization and analysis
Andrew Waterhouse James Cuff
http://www.jalview.org/version118/documentation.html
http://www.jalview.org/
General feature format FASTA format Clustal file format
Jpred
protein secondary structure prediction server
http://www.compbio.dundee.ac.uk/jpred4/about.shtml
KANT
computer algebra software
Technische Universität Berlin
GNU/Linux macOS Microsoft Windows
http://page.math.tu-berlin.de/~kant/KASH/pdf/kash3intro.pdf
http://www.math.tu-berlin.de/~kant/kash.html
KIVA
Computational Fluid Dynamics software
Los Alamos National Laboratory
Fortran Fortran 95
http://www.lanl.gov/projects/feynman-center/deploying-innovation/intellectual-property/software-tools/kiva/index.php
Kekulé Program
chemistry software
Kepler scientific workflow system
software application for analyzing and modeling scientific data
Berkeley Software Distribution
R
University of California, Davis University of California, Santa Barbara University of California, San Diego
Java
Microsoft Windows macOS GNU/Linux
https://code.kepler-project.org/code/kepler-docs/trunk/outreach/documentation/shipping/2.5/UserManual.pdf
https://kepler-project.org/
KiSAO
ontology and software
http://co.mbine.org/standards/kisao
Kinemage
interactive graphic scientific illustration
http://kinemage.biochem.duke.edu
LISE++
spectrometry software
freeware
C++
http://lise.nscl.msu.edu
LONI Pipeline
scientific workflow software
freeware
Java Runtime Environment
Java
Linux macOS Microsoft Windows
http://pipeline.loni.usc.edu/learn/user-guide/
http://pipeline.loni.usc.edu/
Laboratory Unit for Computer Assisted Surgery
for virtual surgical planning
LandView
viewer for GIS data
United States Census Bureau
https://www.census.gov/geo/landview/
Language Acquisition Device
computer program , software , and language acquisition device
King's College London
Lead Finder
computational chemistry application
MAFFT
multiple alignment software for amino acid or nucleotide sequences
Berkeley Software Distribution
macOS Microsoft Windows GNU/Linux
http://mafft.cbrc.jp/alignment/software/
MAXQDA
software program designed for computer-assisted qualitative and mixed methods data, text and multimedia analysis in academic, scientific, and business institutions
proprietary license
macOS Microsoft Windows
http://www.maxqda.com/download/manuals/MAX12_manual_eng.pdf
http://www.maxqda.com/
M2k Excel Binary File Format Office Open XML file formats Advanced Video Coding QuickTime File Format MPEG program stream Audio Video Interleave M4V 3GP and 3G2 Windows Media Video File Format Family Portable Document Format Microsoft Word Binary File Format OpenDocument Text, version 1.0 Rich Text Format Statistical Package for the Social Sciences data file SubRip RIS plain text
M2k
MEGAN
metagenomic analysis software
Java
http://ab.inf.uni-tuebingen.de/software/megan6/
MELCOR
software
Sandia National Laboratories
http://energy.sandia.gov/energy/nuclear-energy/nuclear-energy-safety-technologies/melcor/
MEME suite
sea shanties and karens
National Institutes of Health
http://meme-suite.org/
FASTA format Clustal W
MLwiN
statistical software
University of Bristol
http://www.bristol.ac.uk/cmm/software/mlwin/download/manuals.html
http://www.bristol.ac.uk/cmm/software/mlwin/
MODELLER
software for homology modeling
University of California, San Francisco
Microsoft Windows macOS GNU/Linux Unix
https://salilab.org/modeller/manual/
https://salilab.org/modeller/
MUMmer
software for sequence alignment
Artistic License
C C++
http://mummer.sourceforge.net/manual/
http://mummer.sourceforge.net/
MUSCLE
sequence alignment software
public-domain software
C++
http://www.drive5.com/muscle
FASTA format
FASTA format PHYLIP file format
MacVector
molecular biology software
proprietary license
MacVector
macOS
http://www.macvector.com
Maestro
publicly available version of the software used by the NASA Mars Exploration Rover team
Jet Propulsion Laboratory
Java
GNU/Linux Mac OS X Panther Windows XP Windows 2000
https://mars.nasa.gov/mer/relatedsites/
MapleSim
multi-domain modeling and simulation software
proprietary license
Waterloo Maple
http://www.maplesoft.com/products/maplesim/index.aspx
Mars regional atmospheric modeling system
software that simulates the circulations of the Martian atmosphere
http://www.boulder.swri.edu/~rafkin/
Mascot
software that uses mass spectrometry data to identify proteins from peptide sequence databases
Linux
http://www.matrixscience.com/
Mascot Generic Format
MassMatrix
data analysis software
proprietary license
http://www.massmatrix.bio/wp-content/uploads/2015/02/MassMatrix_PC_GUI_Manual.pdf
http://www.massmatrix.bio/
MasterPlex QT
curve-fitting software
proprietary license
Hitachi Software Engineering
https://psg.hitachi-solutions.com/masterplex
MasterPlex ReaderFit
software
proprietary license
Hitachi Software Engineering
http://www.MiraiBio.com/Elisa-Curve-Fit
Math-o-mir
software tool for mathematical equations
MIT License
C++
Windows 2000 Windows XP Windows Vista Windows 7 Windows 8 Windows 10
http://gorupec.awardspace.com/MathomirManual.pdf
http://gorupec.awardspace.com/mathomir.html
MathMagic
software for editing mathematical equations
Microsoft Windows macOS Android iOS
http://www.mathmagic.com
MathMagic equation File
MathMagic equation File
MeVisLab
cross-platform application framework for medical image processing and scientific visualization
proprietary license
2.7
MeVis Medical Solutions
C++
https://www.mevislab.de/
MedCalc
statistical software
proprietary license
https://www.medcalc.org/manual/index.php
https://www.medcalc.org/
Office Open XML Spreadsheet Document, Transitional, ISO/IEC 29500:2008 OpenDocument Spreadsheet, version 1.0 dBASE Table File Format Family text file Data Interchange Format
Mercury
crystallography software
Cambridge Crystallographic Data Centre
Windows 7 Windows 8 Windows 10 GNU/Linux macOS
https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mercury/
Metascape
gene annotation and analysis software
freeware
GNF
http://metascape.org
Microsoft Math Solver
MS Windows application for solving maths problems
freeware
1.0.210
Microsoft
Android
Microsoft Math worksheet
Microsoft Math worksheet
Mind's Eye
video analysis software
http://www.darpa.mil/Our_Work/I2O/Programs/Minds_Eye.aspx
MochiView
genomic sequence browsing software
University of California, San Francisco
Java
http://www.johnsonlab.ucsf.edu/s/MochiView_Manual_v145.pdf
http://www.johnsonlab.ucsf.edu/mochi/
Mocolo
video analysis software
Model for Prediction Across Scales
simulation software
National Center for Atmospheric Research
https://mpas-dev.github.io/
MolIDE
software for comparative modeling of protein structures
Fox Chase Cancer Center
Molden
molecular and electronic structure software
Center for Molecular and Biomolecular Informatics
Microsoft Windows Linux macOS IRIX SunOS Solaris
http://cheminf.cmbi.ru.nl/molden/
Protein Data Bank Molden format Molden OpenGL model
Molden format Molden OpenGL model
Molecular Evolutionary Genetics Analysis
software for statistical analysis of molecular evolution
Pennsylvania State University
http://www.megasoftware.net/web_help_7/helpfile.htm#hc_first_time_user.htm
http://www.megasoftware.net
Monte Carlo N-Particle Transport Code
software package for simulating nuclear processes
Los Alamos National Laboratory
Fortran
https://laws.lanl.gov/vhosts/mcnp.lanl.gov/mcnp_manual.shtml
http://mcnpx.lanl.gov/ https://mcnp.lanl.gov
Moog
astronomical software package
Fortran
http://www.as.utexas.edu/~chris/moog.html
Morphobank
web application for collaborative evolutionary research
https://morphobank.org/themes/default/graphics/pdf/quick_start_guide.pdf
https://morphobank.org/
MountainsMap
micro-topography software published by Digital Surf
Digital Surf
Microsoft Windows
http://www.digitalsurf.com/en/mntkey.html http://www.digitalsurf.fr/en/platform0.html
text file Windows Bitmap JPEG File Interchange Format (JFIF) TIFF Portable Network Graphics 3D Manufacturing Format Virtual Reality Modeling Language STereoLithography
MovAlyzeR
software package for handwriting movement analysis
C++
http://www.neuroscript.net/help/webframe.html
http://www.neuroscript.net/movalyzer.php
MyDirectives
digital cloud-based advance medical directives platform
Mycin
early expert system with a focus on medical research
NAMD
molecular dynamics simulation software
2.10
University of Illinois Urbana–Champaign
C++
http://www.ks.uiuc.edu/Research/namd/current/ug/
http://www.ks.uiuc.edu/Research/namd
NAVGEM
global numerical weather prediction computer simulation
NCSS
statistical software
https://www.ncss.com/software/ncss/ncss-documentation/
http://www.ncss.com/software/ncss
ACCDB File Format Family dBASE Table File Format Family Office Open XML Spreadsheet Document, ECMA-376 1st Edition MATLAB M-File R Data Format Family
NEMO
astronomy software
3.3.2
C Fortran C++
http://admit.astro.umd.edu/nemo/manual/nemo.html
http://admit.astro.umd.edu/nemo/
NICMOSlook
software to analyze spectral data obtained with the NICMOS spectrometer
Space Telescope European Coordinating Facility
Interactive Data Language
NLPQLP
Fortran subroutine that solves smooth nonlinear programming problems
NNPDF
software
http://nnpdf.hepforge.org
NONMEM
software for population pharmacokinetic modeling
University of California, San Francisco
https://nonmem.iconplc.com/nonmem710/intro7.pdf
NPSOL
software package for solving constrained optimization problems
proprietary license
Fortran
http://www.ccom.ucsd.edu/~peg/papers/npdoc.pdf
http://www.sbsi-sol-optimize.com/asp/sol_product_npsol.htm
NanoLanguage
simulation software for nanoscale systems
National Integrated Ballistic Information Network
computer network
Naval Observatory Vector Astrometry Subroutines
astronomy software library
United States Naval Observatory
C
http://aa.usno.navy.mil/software/novas/novas_info.php
Newbler
software package for de novo DNA sequence assembly
454 Life Sciences
Linux
FASTA format FASTQ format
NinJo
meteorological software
Deutscher Wetterdienst Meteorological Service of Canada Danish Meteorological Institute Federal Office of Meteorology and Climatology MeteoSwiss Bundeswehr
Java
GNU/Linux Microsoft Windows
http://www.ninjo-workstation.com/
Nmrpipe
data processing software for nuclear magnetic resonance
https://www.ibbr.umd.edu/nmrpipe/install.html
NoeClone
software
http://www.noegen.com
NuCalc
graphing calculator software
Microsoft Windows macOS iOS
http://www.pacifict.com/
Nukemap
unclassified nuclear weapons effects data map software
Alex Wellerstein
http://www.nuclearsecrecy.com/nukemap
OE-Cake!
2D fluid physics sandbox software
Microsoft Windows
http://www.prometech.co.jp/
OELib
cheminiformatics software library
C++
OLGA
software modelling tool for transportation of oil, natural gas and water in the same pipeline
proprietary license
Equinor ASA SINTEF
https://www.software.slb.com/products/olga
OLI Analyzer
software used for simulating aqueous-based chemical systems
proprietary license
https://www.olisystems.com/oli-studio-analyzers-scalechem
OLIGO Primer Analysis Software
tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes
Microsoft Windows macOS
http://oligo.net/oligo_7_manual.pdf http://www.oligo.net/oligo_7_manual.pdf
http://oligo.net/
ORTEP
computer program and software
Oak Ridge National Laboratory
Openlab
software for 2D microscope image processing
proprietary license
http://www.icd.eu/produkte/openlab-cds.html
Optica Optics Software
optical design software program
http://www.opticasoftware.com/
Origin
scientific graphing and data analysis software by OriginLab Corporation
proprietary license
2023
opj
Microsoft Windows
http://www.originlab.com
Origin Project Origin Function Plot Origin Fitting Function Definition File
Origin Project Origin Function Plot Origin Fitting Function Definition File
Orthopaedic Studio
software for quantitative hip examinations
OsiriX
http://orthostudio.spectronic.se
Osteoware
data recording software for human skeletal material
http://osteoware.si.edu/
Overflow
fluid dynamics simulation software
https://overflow.larc.nasa.gov/home/users-manual-for-overflow-2-2/
https://overflow.larc.nasa.gov
PARATEC
physics software
Lawrence Berkeley National Laboratory
http://www.nersc.gov/users/software/applications/materials-science/paratec/
PASS Sample Size Software
sample size software tools
proprietary license
NCSS
Microsoft Windows
http://www.ncss.com/ https://www.ncss.com/software/pass/
PDBREPORT
database of anomalies and errors in Protein Data Bank
http://swift.cmbi.ru.nl/gv/pdbreport
PLINK
whole genome association analysis toolset
C C++
http://zzz.bwh.harvard.edu/plink/
PROLITH
photolithography simulation software
Chris Mack
https://www.kla-tencor.com/Virtual-Lithography/dsmprolith.html
PSF Lab
microscope software
freeware
http://onemolecule.chem.uwm.edu/software
PSI Protein Classifier
software
PSI-Plot
data analysis and technical plotting software
http://www.polysoftware.com/psiplot.htm
PSIPRED
software
University College London
C
Windows 2000
http://bioinf.cs.ucl.ac.uk/psipred/
PSORT
bioinformatics software
Parasurf
molecular modelling software
Linux
http://www.ceposinsilico.de/pdf/ParaSurf12.pdf
http://www.ceposinsilico.de/products/parasurf.htm
PatternHunter
homology search instrument software
PeakFit
automated nonlinear peak separation and analysis software package
proprietary license
Microsoft Windows
http://www.systat.com/products/PeakFit/
Petrel
software for exploration of petroleum and gas reserves
proprietary license
Schlumberger
PhotoModeler
stereophotogrammetry software
proprietary license
http://www.photomodeler.com
JPEG File Interchange Format (JFIF) TIFF Windows Bitmap PCX file format family Truevision TGA Portable Network Graphics PICT Photoshop File Format Portable Pixmap, text variant MacPaint Interchange File Format CALS Raster file format Photo CD Silicon Graphics Image JP2 HD Photo QuickTime File Format MPEG-4 Part 14 Audio Video Interleave Windows Media Video File Format Family 3GP and 3G2 MPEG-1 program stream Drawing Interchange File Format Family Wavefront .obj file .3ds comma-separated values
.3ds Rhino 3D Model file format family comma-separated values Drawing Interchange File Format Family Filmbox Initial Graphics Exchange Specification Keyhole Markup Language Keyhole Markup Language Zipped LAS file format Wavefront .obj file Recon Points STereoLithography Virtual Reality Modeling Language
Phrap
software for DNA sequence assembly
Philip Palmer Green
C
macOS Berkeley Software Distribution HP-UX Tru64 UNIX IBM AIX Linux Microsoft Windows IRIX Solaris
http://bozeman.mbt.washington.edu/consed/consed.html
Phred base calling
software for DNA sequencing analysis
Philip Palmer Green
C
macOS Berkeley Software Distribution HP-UX Tru64 UNIX IBM AIX Linux Microsoft Windows IRIX Solaris
http://www.phrap.com/phred/
PhyloXML
XML language for the analysis, exchange, and storage of phylogenetic trees
phyloxml
text/x-phyloxml+xml
http://www.phyloxml.org/
Phylogenetic Analysis Using Parsimony *and other methods
software
http://paup.csit.fsu.edu/
Nexus file
Phyloscan
software for sequence motifs in intergenic regions
Wadsworth Center New York State Department of Health
http://ccmbweb.ccv.brown.edu/cgi-bin/phyloscanV2.pl
Phyre / Phyre2
software for protein structure prediction
http://www.sbg.bio.ic.ac.uk/phyre2
Physicians' Information and Education Resource
software
http://pier.acponline.org
PiHex
software for calculating the bits of Pi
PicoScope
oscilloscope software application
proprietary license
Pico Technology
Visual C++
Microsoft Windows macOS Debian Ubuntu
Plotly
online analytics and data visualization tool
2.20.0
tenacity six tinycolor2 Mapbox GL JS @plotly/d3 @plotly/d3-sankey @plotly/d3-sankey-circular @turf/area @turf/bbox @turf/centroid canvas-fit color-alpha color-normalize color-parse color-rgba country-regex d3-force d3-format d3-geo d3-geo-projection d3-hierarchy d3-interpolate d3-time d3-time-format fast-isnumeric gl-mat4 gl-text glslify has-hover has-passive-events is-mobile mouse-change mouse-event-offset mouse-wheel native-promise-only parse-svg-path point-in-polygon polybooljs probe-image-size regl regl-error2d regl-line2d regl-scatter2d regl-splom strongly-connected-components superscript-text svg-path-sdf to-px topojson-client webgl-context world-calendars
Python JavaScript Julia R
cross-platform
https://plot.ly/ https://github.com/plotly/plotly.js#readme
PowerLab
Australian data research company
ADInstruments
Praat
computer software for the analysis of speech
GNU General Public License, version 3.0 or later
6.4.19
Paul Boersma
C Objective-C C++
Microsoft Windows Unix macOS
https://www.fon.hum.uva.nl/praat/
Praat TextGrid
Praat TextGrid
Predictor@home
BOINC based volunteer computing project to predict protein structure
http://predictor.chem.lsa.umich.edu/
Primer Premier
software for the design and analysis of PCR primers
Premier Biosoft
http://www.premierbiosoft.com http://www.premierbiosoft.com/primerdesign/index.html
ProStat
statistical software
Windows 98 Windows Vista Windows 7 Windows 8
http://www.polysoftware.com/index.htm
ASCII dBASE Table File Format Family Data Interchange Format comma-separated values
ASCII dBASE Table File Format Family Data Interchange Format
Protomap
proteomics software
Benjamin Cravatt
http://www.scripps.edu/cravatt/protomap/
Psychtoolbox for MATLAB
software
http://psychtoolbox.org/
PupaSuite
web-based SNP analysis tool
Pwpaw
software
http://users.wfu.edu/natalie/papers/pwpaw/man.html
PyQuante
Open-source quantum chemistry software
http://pyquante.sourceforge.net/
Q-systems
software
QDA Miner
qualitative data analysis software
proprietary license
Provalis Research
Microsoft Windows
http://www.provalisresearch.com/
Quickfield
finite element analysis software package
Microsoft Windows
http://www.quickfield.com/
RAPTOR
protein threading software
Microsoft Windows Linux
http://www.bioinfor.com/raptor
REDCap
a browser-based software for metadata-driven electronic data capture
end-user license agreement
PHP
https://www.project-redcap.org/
RELAP5-3D
1997 software , from 1997
Idaho National Laboratory
Fortran
http://www.inl.gov/relap5/
RMCProfile
Reverse Monte Carlo for crystalline and disordered materials
Oak Ridge National Laboratory National Institute of Standards and Technology University of Cambridge University of Oxford
http://www.rmcprofile.org/Main_Page
RadExPro seismic software
seismic processing software
Microsoft Windows
RaptorX
software for protein modeling and analysis
http://raptorx.uchicago.edu/
RealSky
digital photographic sky atlas
Recombination detection program
computer program and software
RedShift
planetarium software created by Maris Multimedia
8
personal computer iOS Android
iOS Android
https://www.redshift-live.com/ext/en/
RefDB
NMR spectroscopy database of carefully corrected or re-referenced chemical shifts
http://refdb.wishartlab.com/
Refeus
software tool that supports the entire work process from collecting and managing content and sources to writing and publishing scientific documents and publications
Linux macOS Microsoft Windows
https://www.refeus.de
Regional Atmospheric Modeling System
software
William R. Cotton Roger A. Pielke
http://www.atmet.com/html/docs/rams/rams_techman.pdf
http://rams.atmos.colostate.edu/detailed.html
Registax
image processing software for amateur astrophotographers
freeware
Microsoft Windows
http://www.astronomie.be/registax
RoboGEO
geocoding software program
http://robogeo.com/home/
RobotML
XML-based markup language that is used for communication between autonomous mobile robots and robot components
Munich University of Applied Sciences
Rosalind
educational website and progamming chrestomathy for bioinformatics
http://rosalind.info http://rosalind.info/problems/locations/
RunGEM
software
Gempack
http://www.copsmodels.com/gprgem.htm
SEQUEST
software for Microsoft Windows and Linux
Microsoft Windows Linux
https://assets.thermofisher.com/TFS-Assets/CMD/manuals/Man-XCALI-97160-SEQUEST-331-User-ManXCALI97160-B-EN.pdf
http://www.thermo.com/com/cda/product/detail/0,,16483,00.html?CA=bioworks
SESOIL
software , from 1981
United States Environmental Protection Agency
Fortran
SGS Genesis
software for the modelling of mineral resources
SGS S.A.
http://www.geostat.com/genesis
SHARC molecular dynamics software
molecular dynamics software
Fortran
Linux
http://sharc-md.org/
SHELX
set of crystallography programs
SHELX-76
George M. Sheldrick
http://shelx.uni-goettingen.de/shelxl_user_guide.pdf
http://shelx.uni-goettingen.de/
Crystallographic Information File SHELX output
SHELX output
SHELXL
software for the refinement of crystal structures
George M. Sheldrick
http://shelx.uni-goettingen.de/shelxl_user_guide.pdf
http://shelx.uni-goettingen.de/
SHELXT
small molecule structure solution program
George M. Sheldrick
http://shelx.uni-goettingen.de/shelxt_keywords.php
SHIFTCOR
biological database and software
SIMAP
BOINC based volunteer computing project
https://cube.univie.ac.at/resources/simap http://mips.gsf.de/simap/
SIMION
ion optics simulation program
proprietary license
Microsoft Windows
http://simion.com/
SMS
software for building and simulating surface water models
Aquaveo
http://aquaveo.com/software/sms-surface-water-modeling-system-introduction
SMS Material
SMS Material
SNARK
computer program
Mozilla Public License
SRI International
Common Lisp
http://www.ai.sri.com/~stickel/snark.html
SOCET SET
software application
BAE Systems
http://www.socetset.com
SOFA
astronomy software
Fortran C
http://www.iausofa.org/
SPEED2000
software for electromagnetic simulation for the analysis and design of high-speed electronic systems
Sigrity
http://www.sigrity.com/products/speed2000/spd2k.htm
SRM Engine Suite
engineering software
proprietary license
https://cmclinnovations.com/products/srm/
STATISTICA
analytics software package
12.6
Dell Inc. StatSoft
x86 x86-64
Microsoft Windows
http://www.statsoft.com/
STATISTICA Report File
STATISTICA Report File
STING
software for analysis of the relationship between protein sequence, structure, function, and stability
http://www.cbi.cnptia.embrapa.br/SMS
SahysMod
agricultural software
Delphi
Microsoft Windows
https://www.waterlog.info/pdf/sahysmod.pdf
http://www.waterlog.info/sahysmod.htm
SaltMod
agricultural software
Delphi
Microsoft Windows
http://www.waterlog.info/saltmod.htm
SciCast
collaborative platform for science and technology forecasting
George Mason University
http://scicast.org
Scigress
software for molecular modelling
Fujitsu
C++
http://www.scigress.com
Seasonal Attribution Project
BOINC based volunteer computing climate'prediction.net subproject
Serpent
computational physics program
VTT Technical Research Centre of Finland
C
http://montecarlo.vtt.fi/download/Serpent_manual.pdf
http://montecarlo.vtt.fi/
Shadows
software package for the calculation and drawing of sundials and astrolabes
Windows 10 Windows 8 Windows 7 Windows Vista
https://www.shadowspro.com/en/user-manual.html
https://www.shadowspro.com/en/index.html
Short Oligonucleotide Analysis Package
bioinformatics software tools
http://soap.genomics.org.cn/
SigmaPlot
software package for scientific graphing and data analysis
Microsoft Windows
http://www.sigmaplot.com/products/sigmaplot/sigmaplot-details.php https://systatsoftware.com/products/sigmaplot/
text file comma-separated values Data Interchange Format Lotus 1-2-3 Worksheet file format, version 4-5 Statistical Analysis System data set (Windows)
JPEG File Interchange Format (JFIF) GIF Portable Network Graphics TIFF Windows Bitmap Windows Metafile Windows Enhanced Metafile Portable Document Format Photoshop File Format Encapsulated PostScript
Simcyp Simulator
modelling and simulation platform
https://www.certara.com/software/physiologically-based-pharmacokinetic-modeling-and-simulation/simcyp-simulator/?ap%5B0%5D=PBPK
Simmcast
object-oriented simulation framework for protocol and network research
Singularity
open-source container software for scientific environments
3-clause BSD License
3.8.7
Go C
Linux
https://apptainer.org/docs-legacy/
https://apptainer.org/
Sirius visualization software
molecular modelling and analysis system
San Diego Supercomputer Center
http://sirius.sdsc.edu
Sky Map
planetarium software application
Apache License
1.9.2
Google
Android
Android
https://github.com/sky-map-team/stardroid https://play.google.com/store/apps/details?id=com.google.android.stardroid&hl=en
Skyglobe
astronomy program
freeware
MS-DOS Microsoft Windows
http://adamhome.com/skyglobe.htm
Snack Sound Toolkit
software
Royal Institute of Technology
http://www.speech.kth.se/snack/man/snack2.2/python-man.html
http://www.speech.kth.se/snack/
Broadcast Wave Format Sun Microsystems audio file Audio Interchange File Format Family MPEG-1 Audio Layer III HD
Snagger
software program for selecting tag SNPs using pairwise r2 linkage disequilibrium
MIT License
http://snagger.sourceforge.net/
SnoRNA prediction software
software
Soaplab
software for Java Virtual Machine
European Bioinformatics Institute
Java Virtual Machine
http://soaplab.sourceforge.net/soaplab1/
Solarsoft
software
Lockheed Martin
http://www.lmsal.com/solarsoft/
Space Telescope Science Data Analysis System
astronomical software
Space Telescope Science Institute
http://www.stsci.edu/institute/software_hardware/stsdas
SplitsTree
software
Microsoft Windows Linux macOS
http://ab.inf.uni-tuebingen.de/software/megan4/download1.0/V1_0/manual.pdf/view
http://www.splitstree.org
Starlight Information Visualization System
visualization software
Pacific Northwest National Laboratory
https://starlight.pnnl.gov/
Starlink Project
UK astronomical computing project
http://starlink.eao.hawaii.edu/starlink
Starry Night
planetarium software
http://www.starrynight.com/
StatPlus
software product for basic univariate and multivariate statistical analysis
Microsoft Windows
http://www.analystsoft.com/en/products/statplus/
StatXact
statistical software package
Cytel
C
Microsoft Windows
http://www.cytel.com/software/statxact
Statgraphics
software
18.1.05
Microsoft Excel
http://statgraphics.com/
StatGraphics Data File
Stemloc
software for pairwise RNA structural alignment
https://biowiki.org/wiki/index.php/Stemloc_Tutorial
http://biowiki.org/StemLoc
Stockholm format FASTA format
Stockholm format
Stencil code
class of algorithms
Streamer
radiative transfer code
http://stratus.ssec.wisc.edu/streamer/userman.pdf
http://stratus.ssec.wisc.edu/streamer/
Surface Evolver
software for computational fluid dynamics
freeware
C
Linux Microsoft Windows macOS Unix
http://facstaff.susqu.edu/brakke/evolver/downloads/manual270.pdf
http://www.susqu.edu/facstaff/b/brakke/evolver/evolver.html
Pixar picture Object File Format PostScript Softimage PIC
Surgical segment navigator
surgical simulation software
Carl Zeiss AG
https://marmulla.com/compengl.htm
Sysquake
numerical computing software
6.5
http://www.calerga.com/products/Sysquake/
Systems Tool Kit
astrodynamics computer program from Analytical Graphics, Inc
Analytical Graphics
http://www.agi.com/stk
STK Torque format STK data (generic) STK Azimuth-Elevation Mask format STK Attitude format STK Sensor Pointing format STK Facility Network STK Great Arc Propagator format STK database update information STK Interval List format STK Ephemeris format STK Body Mask format STK Vector format STK Propagator format
STK Torque format STK data (generic) STK Azimuth-Elevation Mask format STK Attitude format STK Sensor Pointing format STK Facility Network STK Great Arc Propagator format STK database update information STK Interval List format STK Ephemeris format STK Body Mask format STK Vector format STK Propagator format
T-REX
software for inferencing, validation and visualization of phylogenic trees
http://www.trex.uqam.ca/
Newick tree format
TI InterActive!
computer algebra software
Texas Instruments
http://education.ti.com/educationportal/sites/US/productDetail/us_ti_interactive.html
TI Interactive Workbook
TI Interactive Workbook
TITAN2D
geoflow simulation software
http://www.gmfg.buffalo.edu
TRACE
orbit determination program
The Aerospace Corporation
TRAMO
statistical software
Bank of Spain
http://www.bde.es/webbde/es/secciones/servicio/software/econom.html
TableCurve 2D
curve-fitting software
http://www.systat.com/products/SigmaPlot/
TableCurve 3D
software
http://www.systat.com/products/SigmaPlot/
Tanagra
machine learning software
open source
1.4.50
Lumière University Lyon 2
Delphi
Microsoft Windows
https://tanagra-machine-learning.blogspot.com/
TaveRNA
software
Simon Fraser University
http://compbio.cs.sfu.ca/taverna
Techlog
software for wellbore data analysis
http://www.slb.com/Techlog
Tecplot
family of visualization & analysis software tools
Tecplot (United States)
https://archive.org/details/manualzilla-id-5758652
https://www.tecplot.com/
TecPlot ASCII Tecplot Macro Tecplot Layout Tecplot Layout Package Hierarchical Data Format
TellStar
first graphical astronomy software
The Accelrys Enterprise Platform
data management platform
The Geochemist's Workbench
software tools for solving problems in aqueous chemistry
University of Illinois Urbana–Champaign
Microsoft Windows
https://www.gwb.com/pdf/GWB12/GWBessentials.pdf
http://www.gwb.com
The Proteolysis Map
integrated web resource focused on proteases
Sanford Burnham Prebys Medical Discovery Institute
http://sonny.burnham.org/proteases/
TheSky
astronomy software
proprietary license
Software Bisque
http://www.bisque.com
TimeTree
database of times of divergence in the tree of life
freeware
http://www.timetree.org/
Tinker
molecular dynamics simulation software
8.2.1
https://dasher.wustl.edu/tinker/downloads/guide.pdf
https://www.tinkertools.org/
TopFIND
knowledgebase of protein termini
University of British Columbia
http://clipserve.clip.ubc.ca/topfind
TracePro
optical engineering software
Transana
Transana is a free, open source program offered by the University of Wisconsin-Madison Center for Education Research for transcribing and analyzing la
GNU General Public License
C++ Python
macOS Microsoft Windows
http://www.transana.org/
TranscriberAG
free software; tool for the transcription and annotation of speech signals for linguistic research
GNU General Public License
1.5.1
Tcl C
macOS Microsoft Windows Linux
http://transag.sourceforge.net/
Transcriber AG TAG Format
Transcriber AG TAG Format
Tree puzzle
software
http://www.tree-puzzle.de/
Treefinder
for the likelihood-based reconstruction of phylogenetic trees from molecular sequences
Gangolf Jobb
http://www.treefinder.de/
UCSF Chimera
software for visualization and analysis of molecular structures
University of California, San Francisco
http://www.cgl.ucsf.edu/chimera/index.html http://www.rbvi.ucsf.edu/chimera/
Protein Data Bank CCP4 simplified molecular input line entry specification XYZ file format MDL Molfile Stockholm format Digital Asset Exchange Virtual Reality Modeling Language
UTOPIA
bioinformatics tool
Ubuntu-Med
software
Unified Victim Identification System
database system for critical fatality management
Office of Chief Medical Examiner of the City of New York
Unistat
statistical data analysis software
https://www.unistat.com/
UrQMD
Monte Carlo simulation package for Proton+Proton, Proton+nucleus and nucleus+nucleus interactions
Goethe University Frankfurt
Fortran
https://vfs.fias.uni-frankfurt.de/f/b4416cdac5/?raw=1
http://www.th.physik.uni-frankfurt.de/~urqmd http://urqmd.org
VISQ
scientific educational software
http://www.modelciencias.furg.br/bin/ferramentas/semi/visq.php
Vaa3D
software
Validis
software
Verbal-Robot
chatterbot
ViEWER
software to create virtual displays
C++
Microsoft Windows
http://webpages.uidaho.edu/~bdyre/viewer.htm
Vienna Ab-initio Simulation Package
software package for condensed matter physics
VASP Software GmbH
Fortran
https://www.vasp.at
Vienna RNA Package
bioinformatics library and set of programs for RNA secondary structure analysis and prediction
free software license
2.1.9
Unix Microsoft Windows
C Perl Python
http://www.tbi.univie.ac.at/RNA/
Virtual Cell
software platform for modeling and simulation of living organisms, primarily cells
MIT License
University of Connecticut Health Center
Java
Microsoft Windows
http://vcell.org/webstart/VCell_Tutorials/VCell_Quickstart_6.pdf
http://vcell.org
Systems Biology Markup Language
Systems Biology Markup Language Nearly Raw Raster Data
Vnmr
software for controlling nuclear magnetic resonance spectrometers
proprietary license
Varian, Inc.
Solaris
http://www.varianinc.com/cgi-bin/nav?products/nmr/software/vnmrj&cid=KMPLINPJFM
Voxel-Man
software for the creation and visualization of three-dimensional digital models of the human body
University Medical Center Hamburg-Eppendorf
WAsP
software for wind resource assessment
Technical University of Denmark
http://www.wasp.dk/
WEAP
decision support system software
http://www.weap21.org/
WHAT IF software
molecular modeling and visualization package
Fortran
Linux
http://swift.cmbi.ru.nl/whatif
Protein Data Bank
WIEN2k
software for quantum mechanical calculations on periodic solids
TU Wien
Fortran 90
http://susi.theochem.tuwien.ac.at/
WIMATS
software to transcribe mathematical and scientific text input into braille script for braille presses
Webel Mediatronics Limited
http://www.webelmediatronics.in/brlads/wimats.htm
WMS
hydrology software
Aquaveo
Windows 7 Windows 8 Windows 8.1 Windows 10
http://www.aquaveo.com/wms http://aquaveo.com/wms
ESRI Arc/Info ASCII Grid shapefile Drawing Interchange File Format Family AutoCAD Drawing TIFF JPEG File Interchange Format (JFIF)
WORHP
mathematical software library
European Space Agency
Unix-like operating system
http://www.worhp.de
WUHU
weather data uploading software
Teechart
Microsoft Windows
https://wuhusoftware.azurewebsites.net/
WXP
Science software
http://wxp.unisys.com/
WaveLab
collection of Matlab functions used to implement algorithms related to wavelet analysis
http://www-stat.stanford.edu/~wavelab
WeBWorK
Online homework delivery system
Artistic License
University of Rochester
Perl
http://webwork.maa.org/
Webtag
bioinformatics software
WhiskerControl
research control system
University of Cambridge
C++
Windows NT Windows 2000 Windows XP Windows Vista Windows 7 Windows 8
http://www.whiskercontrol.com
WinGX
for solving, refining and analysing single crystal X-ray diffraction data for small molecules
Windows 2000 Windows XP Windows Vista Windows 7 Windows 8
http://www.chem.gla.ac.uk/~louis/software/wingx/
WinStars
planetarium, ephemeris and solar system simulator
C++
Microsoft Windows Android iOS Linux macOS
https://winstars.net/en
WindSim
wind farm design tool
http://www.windsim.com/products.aspx
Winplot
plotting utility software
C++
Microsoft Windows
http://math.exeter.edu/rparris/winplot.html
WinPlot data (v2) WinPlot data (v3)
WordStat
content analysis and text mining add-on module of QDA Miner
QDA Miner
http://provalisresearch.com/fr/produits/wordstat/ http://www.provalisresearch.com/
WorldWide Telescope
astronomy software
MIT License
Microsoft
C#
Microsoft Windows
http://worldwidetelescope.org
WorldWide Telescope collection WorldWide Telescope Tour
X-12-ARIMA
software package for seasonal adjustment
United States Census Bureau
http://www.census.gov/srd/www/x12a/
XEphem
planetarium software
MIT License
4.2.0
Unix-like operating system
http://www.clearskyinstitute.com/xephem/
http://www.clearskyinstitute.com/xephem/
XLfit
Microsoft Excel-based plug-in which performs regression, curve fitting and statistical analysis
Microsoft Excel
http://www.excelcurvefitting.com/
XSight
discontinuted software for qualitative data analysis
proprietary license
QSR International
http://www.qsrinternational.com/products_xsight.aspx/
Xrate
bioinformatics software
http://biowiki.org/XRATE
Xrate format
Xrate format
Yasara
computer program for molecular visualising, modelling, and dynamics
OpenBabel
C
Microsoft Windows Linux macOS Android
http://www.yasara.org
Protein Data Bank
ZOOMQ3D
software
http://www.oomodels.info/pmwiki/pmwiki.php/Main/OOModelsHome
aTrain
aTrain is a tool for automatically transcribing speech recordings utilizing state-of-the-art machine learning models without uploading any data.
1.1.0
Python
Microsoft Windows
https://github.com/BANDAS-Center/aTrain
aXe Spectral Extraction
software
European Space Agency
http://axe-info.stsci.edu/
artificial intuition
theoretical capacity of AI to develop human intuition
eTBLAST
free text similarity service search engine
https://helioblast.heliotext.com
formatdb
discontinued software tool for molecular bioinformatics
iRows
defunct web-based spreadsheet software
imc FAMOS
software for the analysis, visualization and documentation of measurement data
http://www.imc-famos.de http://www.imcfamos.com/
noScribe
Cutting edge AI technology for automated audio transcription. A nice GUI for OpenAIs Whisper and pyannote (speaker identification)
GNU General Public License, version 3.0
0.5
Python
Microsoft Windows macOS
https://github.com/kaixxx/noScribe/
xaitment
German company
http://www.xaitment.com/
.svg){kind=logo}
.png){kind=logo}
_-_Solar_system_(2).png)
