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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Python Programming Language Resource Report Resource Website 1000+ mentions |
Python Programming Language (RRID:SCR_008394) | programming language, software resource | Programming language for all operating systems that lets users work more quickly and integrate their systems more effectively. Often compared to Tcl, Perl, Ruby, Scheme or Java. Some of its key distinguishing features include very clear and readable syntax, strong introspection capabilities, intuitive object orientation, natural expression of procedural code, full modularity, exception-based error handling, high level dynamic data types, extensive standard libraries and third party modules for virtually every task, extensions and modules easily written in C, C (or Java for Python, or .NET languages for IronPython), and embeddable within applications as a scripting interface. | programming language |
is used by: SciPy is used by: Sumatra is used by: NetPyNE is used by: Wessim is used by: PhenVar is used by: cwltool is used by: kCSD-python is used by: Leginon is used by: DeepNeuro is used by: Phenograph is used by: XDSME is used by: ScaffMatch is used by: PS-Plant Framework is used by: HaTSPiL is used by: SwiftOrtho is used by: ROSE is used by: PyRosetta is used by: PyMC3 is related to: IPython is related to: An Open-Source MATLAB-to-Python Compiler is related to: Cython C-Extensions for Python is related to: Neuroimaging in Python is related to: IPython Notebook is related to: LFPy is related to: CCTop is related to: PPR-Meta is related to: CCPN Analysis is related to: rnaQUAST is related to: MITE-Tracker is related to: COsleep is related to: Anima scripts is related to: Scikit-Criteria is related to: Haystack is related to: mzStudio is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens is required by: VAPPER |
Free, Public, Freely available | nif-0000-30053 | SCR_008394 | SciCrunch Registry | Python3, Python | 2026-10-10 12:44:33 | 2849 | ||||||||
|
IPython Resource Report Resource Website 100+ mentions |
IPython (RRID:SCR_001658) | IP(y) | software resource | A web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. It offers a comprehensive library on top of which more sophisticated systems can be built. The project provides an enhanced interactive environment that includes support for data visualization and facilities for distributed and parallel computation. | publication, authoring tool, rich media, parallel computing, data visualization, python, computing, notebook |
is listed by: FORCE11 is related to: Python Programming Language is related to: IPython Notebook is related to: SciPy has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: California Polytechnic State University; California; USA |
US Department of Energy DE-FG02-03ER25583; DOE-Oak Ridge National Laboratory 4000038129 |
Free, Available for download, Freely available | nlx_153939 | SCR_001658 | SciCrunch Registry | IPython Interactive Computing | 2026-10-10 12:36:08 | 354 | ||||||
|
NetPyNE Resource Report Resource Website 10+ mentions |
NetPyNE (RRID:SCR_014758) | data analysis software, data processing software, network analysis software, software application, software resource | Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks. | Simulation, analysis, neuronal, network, NEURON, simulator, BRAIN Initiative |
uses: Python Programming Language is recommended by: BRAIN Initiative works with: NEURON |
NIBIB EB022903 | DOI:10.7554/eLife.44494.001 | Free, Available for download, Freely available | http://www.neurosimlab.org/netpyne/overview.html | SCR_014758 | SciCrunch Registry | Network development Python package for NEURON | 2026-10-10 12:39:30 | 27 | ||||||
|
Wessim Resource Report Resource Website 1+ mentions |
Wessim (RRID:SCR_002567) | data analysis software, data processing software, sequence analysis software, simulation software, software application, software resource | Software simulator for a targeted resequencing generally known as exome sequencing. Wessim generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation. | resequencing simulator, artificial dna fragments, exome sequencing, next generation sequencing, ngs, python |
uses: Python Programming Language is listed by: OMICtools requires: SAMTOOLS requires: NumPy requires: GemSIM |
PMID:23413434 | Free, Available for download, Freely available | OMICS_00259 | SCR_002567 | SciCrunch Registry | 2026-10-10 12:41:39 | 3 | ||||||||
|
Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | data acquisition software, data or information resource, data processing software, data repository, image acquisition software, portal, service resource, software application, software resource, storage service resource | System designed for automated collection of images from a transmission electron microscope. | automated, collection, acquisition, data, image, electron, microscope |
uses: Python Programming Language has parent organization: Scripps Research Institute |
NCRR RR17573; NIGMS GM61939; NSF DBI0352386; NSF DBI9730056; NSF DBI9904547 |
PMID:15890530 | Free, Available for download, Freely available, Registration suggested | SCR_016731 | SciCrunch Registry | 2026-10-10 12:39:58 | 45 | ||||||||
|
XDSME Resource Report Resource Website 10+ mentions |
XDSME (RRID:SCR_016943) | xdsme | data processing software, image processing software, software application, software resource, software toolkit | Software package of python scripts made to simplify the processing of crystal diffraction images. | simplify, processing, crystal, diffraction, image, data, XDS |
uses: Python Programming Language works with: XDS Program Package |
Free, Available for download, Freely available | SCR_016943 | SciCrunch Registry | XDSME, X-ray Detector Software Made Easier, XDS Made Easier | 2026-10-10 12:40:38 | 15 | ||||||||
|
PPR-Meta Resource Report Resource Website 1+ mentions |
PPR-Meta (RRID:SCR_016915) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, metagenomic, sequence, phage, chromosome, plasmid, fragment, machine, learning |
is related to: Python Programming Language is related to: MATLAB is related to: tensorflow |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/zhenchengfang/PPR-Meta | SCR_016915 | SciCrunch Registry | 2026-10-10 12:39:54 | 4 | |||||||||
|
mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows. | proteomic, data, analysis, visualization, notebooking, mass, spectrometry, modification, gas, phase, fragmentation, behavior |
is listed by: OMICtools is related to: Python Programming Language |
Barr Program in Basic Research ; Dana-Farber Strategic Research Initiative ; Honorable Tina Brozman Foundation for Ovarian Cancer Research ; Michael J. Fox Foundation ; NCI CA042368; NCI CA178860; NCI CA188881 |
PMID:28763045 | Free, Available for download, Freely available | OMICS_26946 | https://omictools.com/mzstudio-tool | SCR_017088 | SciCrunch Registry | 2026-10-10 12:39:57 | 1 | ||||||
|
VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | data analysis software, data processing software, software application, software resource | Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections. | variant, antigen, profiling, data, genome, transcriptome, proteome, gene, expression, infection, Trypanosoma, bio.tools |
is listed by: Debian is listed by: bio.tools requires: Python Programming Language |
Free, Available for download, Freely available | biotools:VAPPER | https://bio.tools/VAPPER | SCR_016993 | SciCrunch Registry | VAP, VariantAntigenProfilingPER | 2026-10-10 12:40:00 | 1 | ||||||
|
rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | data processing software, software application, software resource | Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software. | evaluation, quality, RNA-Seq, assembly, data, transcriptome, assembler, reference, genome, gene, database, raw, read, , bio.tools |
uses: BUSCO is listed by: Debian is listed by: bio.tools is related to: rnaSPAdes is related to: Python Programming Language is related to: SPAdes |
EMC Research and Development Department ; St. Petersburg State University ; Russia |
PMID:27153654 | Free, Available for download, Freely available | biotools:rnaQUASt | https://bio.tools/rnaQUAST | SCR_016994 | SciCrunch Registry | 2026-10-10 12:42:47 | 4 | ||||||
|
ROSE Resource Report Resource Website 50+ mentions |
ROSE (RRID:SCR_017390) | ROSE | data processing software, software application, software resource | To create stitched enhancers, and to separate super enhancers from typical enhancers using sequencing data given file of previously identified constituent enhancers . | Stitched, enhancer, separate, super, sequencing, data, file, identified, previously, constituent |
uses: SAMTOOLS uses: Python Programming Language |
Free, Freely available | SCR_017390 | SciCrunch Registry | Rank Ordering of Super Enhancers, RANK ORDERING OF SUPER-ENHANCERS | 2026-10-10 12:42:43 | 72 | ||||||||
|
SciPy Resource Report Resource Website 10000+ mentions |
SciPy (RRID:SCR_008058) | software application, software resource | A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console. | python, software, open source |
uses: Python Programming Language is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is listed by: SoftCite is related to: IPython is related to: NumPy is related to: IPython Notebook is related to: MNE software is related to: DE-Sim is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens |
Public, Free | nif-0000-10422 | SCR_008058 | SciCrunch Registry | SciPy, Scientific Tools for Python | 2026-10-10 12:44:32 | 16188 | ||||||||
|
PyRosetta Resource Report Resource Website 10+ mentions |
PyRosetta (RRID:SCR_018541) | software application, software resource, standalone software | Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions. | Molecular modeling, custom structure prediction, design algorithm, energy function, scoring function, bio.tools |
uses: Python Programming Language is listed by: bio.tools is listed by: Debian is related to: Rosetta has parent organization: Johns Hopkins University; Maryland; USA |
NIGMS R01 GM078221; NIGMS R01 GM73151; NSF 0846324 |
PMID:20061306 | Free, Freely available | biotools:pyrosetta | https://bio.tools/pyrosetta | SCR_018541 | SciCrunch Registry | Python Rosetta | 2026-10-10 12:44:56 | 25 | |||||
|
Cython C-Extensions for Python Resource Report Resource Website 100+ mentions |
Cython C-Extensions for Python (RRID:SCR_008466) | software resource | Cython is a language that makes writing C extensions for the Python language as easy as Python itself. Cython is based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. The Cython language is very close to the Python language, but Cython additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, and for fast C modules that speed up the execution of Python code. Sponsor. Google and Enthought funded Dag Seljebotn to greatly improve Cython integration with NumPy. Kurt Smith and Danilo Freitas were funded through the Google Summer of Code program to work on improved Fortran and C support respectively. |
is related to: Python Programming Language is required by: TomoMiner |
nif-0000-30401 | SCR_008466 | SciCrunch Registry | Cython | 2026-10-10 12:38:04 | 140 | ||||||||||
|
An Open-Source MATLAB-to-Python Compiler Resource Report Resource Website 1+ mentions |
An Open-Source MATLAB-to-Python Compiler (RRID:SCR_008409) | compiler, software application, software development tool, software resource | OMPC aims to enable reuse of the huge open and free code base of MATLAB on a free and faster growing Python platform. Running Python and MATLAB in a single interpreter avoids issues with running two separate applications. Python adds general purpose programming libraries to the convenient syntax of the language of technical computing. OMPC is not an interpreter, it lets Python to do the work. This means that if Python gets faster OMPC gets faster too. OMPC translates the m-files preserving the structure of the original programs as much as possible. Although OMPC comes with a library that emulates the features of numerical array of MATLAB there is nothing that will stop you from running the translated code the way you like it. This means that you could run the OMPC generated code on IronPython, Jython, PyPy or whatever else if you write your own numerical class. Sponsors: This resource is supported by RIKEN Brain Science Institute. | code, compiler, python, matlab, computng, software, program |
is related to: Python Programming Language is related to: MATLAB |
nif-0000-30104 | SCR_008409 | SciCrunch Registry | OMPC | 2026-10-10 12:38:19 | 2 | |||||||||
|
Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | community building portal, data or information resource, portal, software application, software development environment, software development tool, software resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | SciCrunch Registry | NIPY Community | 2026-10-10 12:38:59 | 27 | ||||
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IPython Notebook Resource Report Resource Website 1+ mentions |
IPython Notebook (RRID:SCR_013984) | software resource, web application | A web application and interactive computational environment where users can combine code execution, rich text, mathematics, plots, and rich media. IPython Notebook consists of two parts, the web application and plain texts. The Ipython Notebook web application is used for interactive authoring of literate computations, in which explanatory text, mathematics, computations, and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place. The plain text documents, called notebooks, record and distribute the results of the rich computations. Saved files in the notebook can be put under version control and shared with colleagues. | web application, computational environment, interactive, Python, code |
is used by: Wakari is listed by: Connected Researchers is related to: IPython is related to: Python Programming Language is related to: Connected Researchers is related to: Wakari is related to: SciPy |
Microsoft ; Alfred P. Sloan Foundation ; Rackspace |
Free, Public | SCR_013984 | SciCrunch Registry | 2026-10-10 12:39:11 | 8 | |||||||||
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ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | data processing software, software application, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | SciCrunch Registry | 2026-10-10 12:42:42 | 1 | ||||||
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Sumatra Resource Report Resource Website 10+ mentions |
Sumatra (RRID:SCR_001381) | electronic laboratory notebook, software application, software resource | A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt. | simulation, analysis, python, numerical simulation, manage, track |
uses: Python Programming Language is listed by: INCF Software Center has parent organization: NeuralEnsemble |
Free, Freely Available | nlx_152549 | SCR_001381 | SciCrunch Registry | Sumatra: automated tracking of scientific computations | 2026-10-10 12:43:10 | 27 | ||||||||
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Short Read Sequence Typing for Bacterial Pathogens Resource Report Resource Website 10+ mentions |
Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) | SRST2 | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. | genotype analysis, illumina sequence data, mlst database, gene sequence, st, reference gene, short read |
uses: Bowtie uses: SAMTOOLS is listed by: Debian is listed by: OMICtools requires: SciPy requires: Python Programming Language |
infectious disease | NHMRC of Australia 1043830; NHMRC of Australia 1061409; NHMRC of Australia 1061435; Victorian Life Sciences Computation Initiative (VLSCI) VR0082 |
PMID:25422674 | Free, Available for download | OMICS_12777 | http://katholt.github.io/srst2/, https://sources.debian.org/src/srst2/ | http://srst.sourceforge.net/ | SCR_015870 | SciCrunch Registry | SRST2: Short Read Sequence Typing for Bacterial Pathogens, Short Read Sequence Typing v2 | 2026-10-10 12:39:41 | 24 |
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