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https://www.sqlite.org/index.html

Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program.

Proper citation: SQLite (RRID:SCR_017672) Copy   

•   Source: SciCrunch Registry

https://www.sutter.com/manuals/P-2000_OpMan.pdf

Microprocessor controlled, CO2 laser based micropipette puller.Default configuration allows fabrication of micropipettes for intracellular recording, patch clamping, microinjection and microperfusion.Can store up to 100 separate programs, each consisting of up to 8 command lines. The five parameters set in each command line allow exquisite control of the micropipette taper geometry. Allows the use of wide range of glass diameters from 0.125 to 1.2 mm.

Proper citation: Sutter: P-2000 Laser Micropipette Puller (RRID:SCR_018640) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/eido/

Software validation tool for Portable Encapsulated Projects or PEPs in python.

Proper citation: eido (RRID:SCR_021076) Copy   

•   Source: SciCrunch Registry

https://github.com/wtsi-hpag/PretextView

Software tool to enable visualization from PretextMap output. Desktop application for viewing pretext contact maps. OpenGL Powered Pretext Contact Map Viewer.

Proper citation: PretextView (RRID:SCR_022024) Copy   

•   Source: SciCrunch Registry

https://knowledge.brain-map.org/celltypes

Software application to examine multimodal data from thousands of cells across 3 mammalian species.

Proper citation: Cell Type Knowledge Explorer (RRID:SCR_022793) Copy   

•   Source: SciCrunch Registry

https://www.millisecond.com/download/

Software tool for designing and administering psychological tests and experiments on computers.

Proper citation: Inquisit LAB (RRID:SCR_022151) Copy   

•   Source: SciCrunch Registry

https://github.com/PeterEckmann1/preprint-match

Software tool to match bioRxiv preprints with their corresponding PubMed paper.

Proper citation: PreprintMatch (RRID:SCR_022302) Copy   

•   Source: SciCrunch Registry

http://www.cgmartini.nl/index.php/downloads/tools/239-insane

Software tool for generating custom membranes for molecular simulations. Software Python script to setup Martini bilayer systems.

Proper citation: insane.py (RRID:SCR_022317) Copy   

•   Source: SciCrunch Registry

https://bbknn.readthedocs.io/en/latest/

Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner.

Proper citation: BBKNN (RRID:SCR_022807) Copy   

•   Source: SciCrunch Registry

https://www.freecad.org/

Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters.

Proper citation: FreeCAD (RRID:SCR_022535) Copy   

•   Source: SciCrunch Registry

https://github.com/kalininalab/d-StructMAn

Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database.

Proper citation: d-StructMAn (RRID:SCR_022534) Copy   

•   Source: SciCrunch Registry

https://github.com/Hi5App

Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration.

Proper citation: Hi5App (RRID:SCR_022819) Copy   

•   Source: SciCrunch Registry

https://github.com/anuprulez/ml-jupyter-notebook

Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning.

Proper citation: Docker based GPU enabled Jupyterlab (RRID:SCR_022695) Copy   

•   Source: SciCrunch Registry

https://github.com/Frederik-D-Weber/zmax_edf_merge_converter

Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format.

Proper citation: zmax_edf_merge_converter (RRID:SCR_022567) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/

Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions.

Proper citation: SigProfilerMatrixGenerator (RRID:SCR_023122) Copy   

•   Source: SciCrunch Registry

https://remm.bihealth.org

Software tool that scores positions in human genome in terms of their regulatory probability. Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases.

Proper citation: ReMM score (RRID:SCR_023095) Copy   

•   Source: SciCrunch Registry

https://www.oracle.com/applications/crystalball/

Software spreadsheet based application for risk measurement and reporting, Monte Carlo simulation, time series forecasting, and optimization.Provides realistic and accessible way of modeling uncertainty, enabling you to measure and report on risk inherent in your key metrics.

Proper citation: Oracle Crystal Ball (RRID:SCR_023226) Copy   

•   Source: SciCrunch Registry

https://drawio-app.com/product/

Software tool as diagramming application that enables collaboration in real time.

Proper citation: draw.io (RRID:SCR_022939) Copy   

•   Source: SciCrunch Registry

https://github.com/sapporo-wes/sapporo-service

Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification.

Proper citation: Sapporo service (RRID:SCR_023202) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/de/de/home/digital-science/thermo-fisher-connect.html

Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment.

Proper citation: ThermoFisher Connect Platform (RRID:SCR_023441) Copy   

•   Source: SciCrunch Registry