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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 | Python3, Python | 2026-08-05 10:45:01 | 2373 | ||||||||
|
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 | IPython Interactive Computing | 2026-08-01 12:01:46 | 341 | ||||||
|
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 | 2026-08-04 09:44:02 | 3 | ||||||
|
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 | Rank Ordering of Super Enhancers, RANK ORDERING OF SUPER-ENHANCERS | 2026-08-04 09:44:09 | 56 | ||||||||
|
PyRosetta Resource Report Resource Website 10+ mentions |
PyRosetta (RRID:SCR_018541) | software application, standalone software, software resource | 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 GM73151; NIGMS R01 GM078221; NSF 0846324 |
PMID:20061306 | Free, Freely available | biotools:pyrosetta | https://bio.tools/pyrosetta | SCR_018541 | Python Rosetta | 2026-08-04 09:44:21 | 20 | |||||
|
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 | SciPy, Scientific Tools for Python | 2026-08-04 09:42:05 | 12935 | ||||||||
|
NetPyNE Resource Report Resource Website 10+ mentions |
NetPyNE (RRID:SCR_014758) | data processing software, software application, data analysis software, software resource, network analysis software | 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 | Network development Python package for NEURON | 2026-08-05 10:46:11 | 26 | ||||||
|
Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | data or information resource, data processing software, data repository, portal, data acquisition software, image acquisition software, software application, software resource, storage service resource, 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 | 2026-08-05 10:46:44 | 42 | ||||||||
|
XDSME Resource Report Resource Website 10+ mentions |
XDSME (RRID:SCR_016943) | xdsme | data processing software, software application, software toolkit, software resource, image processing software | 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 | XDSME, X-ray Detector Software Made Easier, XDS Made Easier | 2026-08-05 10:46:41 | 14 | ||||||||
|
VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | software resource, data processing software, software application, data analysis software | 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 | VAP, VariantAntigenProfilingPER | 2026-08-05 10:46:47 | 1 | ||||||
|
PPR-Meta Resource Report Resource Website 1+ mentions |
PPR-Meta (RRID:SCR_016915) | data processing software, software application, sequence analysis software, data analysis software, 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 | 2026-08-05 10:46:40 | 4 | |||||||||
|
mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | data processing software, software application, data visualization software, data analysis software, 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 |
NCI CA188881; NCI CA178860; NCI CA042368; Dana-Farber Strategic Research Initiative ; Barr Program in Basic Research ; Honorable Tina Brozman Foundation for Ovarian Cancer Research ; Michael J. Fox Foundation |
PMID:28763045 | Free, Available for download, Freely available | OMICS_26946 | https://omictools.com/mzstudio-tool | SCR_017088 | 2026-08-05 10:46:49 | 1 | ||||||
|
Wessim Resource Report Resource Website 1+ mentions |
Wessim (RRID:SCR_002567) | data processing software, software application, simulation software, data analysis software, sequence analysis software, 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 | 2026-08-05 10:43:38 | 3 | ||||||||
|
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 | Cython | 2026-08-01 12:03:45 | 135 | ||||||||||
|
DeepNeuro Resource Report Resource Website 1+ mentions |
DeepNeuro (RRID:SCR_016911) | software toolkit, software resource | Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners. | Design and train neural network architectures, medical imaging, neuroimaging data, neuroimaging |
uses: Python Programming Language is related to: Massachusetts General Hospital has parent organization: Harvard University; Cambridge; United States |
NIDA T90 DA022759; NIDA R90 DA023427; NIH Blueprint for Neuroscience Research ; NIBI ; NIBIB T32 EB1680; NCI U01 CA154601; NCI U24 CA180927; NCI U24 CA180918; NIBIB P41 EB015896 |
PMID:32578020 | Free, Available for download, Freely available | SCR_016911 | 2026-08-02 09:07:34 | 2 | ||||||||
|
PyMC3 Resource Report Resource Website 50+ mentions |
PyMC3 (RRID:SCR_018547) | software toolkit, software resource | Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code. | Bayesian statistical modeling, probabilistic machine learning, advanced Markov chain Monte Carlo, variational fitting algorithm, model specification, Python code | uses: Python Programming Language | DOI:10.7717/peerj-cs.55 | Free, Freely available | SCR_018547 | 2026-08-02 09:07:49 | 64 | |||||||||
|
LFPy Resource Report Resource Website 10+ mentions |
LFPy (RRID:SCR_014805) | software resource, source code | Python package for calculation of extracellular potentials from multicompartment neuron models. LFPy can be used to set up a model, run simulations, and calculate the extracellular potentials arising from activity in the given model neuron. It relies on the Python interface provided by the NEURON simulator. | python, extracellular potential, neuron, model, simulator |
uses: NEURON is related to: Python Programming Language |
PMID:24474916 DOI:10.3389/fninf.2013.00041 |
Open source, Available for download | SCR_014805 | 2026-08-03 09:35:53 | 33 | |||||||||
|
TomoMiner Resource Report Resource Website 1+ mentions |
TomoMiner (RRID:SCR_015045) | software resource, source code | Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging. | analysis platform, cryo electron subtomogram, subtomogram classification, subtomogram alignment, subtomogram averaging, subtomogram analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA requires: Python Programming Language requires: NumPy requires: SciPy requires: LAPACK linear algebra library requires: Cython C-Extensions for Python |
Available for download | biotools:tomominer | https://bio.tools/tomominer | SCR_015045 | 2026-08-03 09:35:59 | 3 | ||||||||
|
kCSD-python Resource Report Resource Website 1+ mentions |
kCSD-python (RRID:SCR_015777) | software resource, source code | Source code for the Python implementation of the kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes. | kernel current source density, 1d, 2d, 3d, python, local field potential, transmembrane current source | uses: Python Programming Language | PMID:22091662 | Free, Available for download | SCR_015777 | kernel current source density method - python, kCSD inverse method, Kernel Current Source Density Method | 2026-08-03 09:36:13 | 7 | ||||||||
|
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 | 2026-08-04 09:44:03 | 1 |
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