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https://woldlab.caltech.edu/wiki/Condor

Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid.

Proper citation: Condor (RRID:SCR_017664) Copy   

•   Source: SciCrunch Registry

https://www.flimfit.org/

Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FLIMfit (RRID:SCR_016298) Copy   

•   Source: SciCrunch Registry

https://github.com/dmis-lab/biobert

Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.

Proper citation: BioBERT (RRID:SCR_017547) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/nbdocker

Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.

Proper citation: nbdocker (RRID:SCR_017159) Copy   

•   Source: SciCrunch Registry

http://www.agriculturalsoftwareconsultants.com/mixitwin

Professional feed formulation software for Windows 10 and Macs by Agricultural Software Consultants Inc. Complete feed formulation solution for professional nutritionists and feed producers. Software offers ingredient databases for various domesticated and wild species.

Proper citation: MixitWin (RRID:SCR_017553) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/HomoeologPrimer

Software tool as script used to design primers for homoeologs, to amplify either homoeolog specific or all homoeologs.

Proper citation: HomoeologPrimer (RRID:SCR_017559) Copy   

•   Source: SciCrunch Registry

https://www.google.com/sheets/about/

Spreadsheet program included as part of free, web-based software office suite offered by Google within its Google Drive service. Service also includes Google Docs and Google Slides, word processor and presentation program respectively.

Proper citation: Google Sheets (RRID:SCR_017679) Copy   

•   Source: SciCrunch Registry

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://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://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://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/eegsynth/eegsynth

Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time.

Proper citation: EEGsynth (RRID:SCR_018732) 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

https://github.com/OpenMendel/MendelIHT.jl

Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs.

Proper citation: MendelIHT.jl (RRID:SCR_018292) 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://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

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://www.acdlabs.com/products/draw_nom/draw/chemsketch/index.php

Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease.

Proper citation: ACD/ChemSketch (RRID:SCR_019272) Copy   

•   Source: SciCrunch Registry

https://github.com/dandi/dandi-cli/

Command line client to facilitate common operations.

Proper citation: dandi-cli (RRID:SCR_019009) Copy   

•   Source: SciCrunch Registry

https://atlasti.com/

Software qualitative analysis tool. Used by researchers and practitioners to uncover and systematically analyze complex phenomena hidden in unstructured data including text, multimedia, geospatial. Provides tools that let the user locate, code, and annotate findings in primary data material, to weigh and evaluate their importance, and to visualize relations between them. Consolidates documents and keeps track of all notes, annotations, codes and memos in all fields that require close study and analysis of primary material consisting of text, images, audio, video, and geo data. Provides analytical and visualization tools designed to open new interpretative views on material.

Proper citation: ATLAS.ti (RRID:SCR_022920) Copy   

•   Source: SciCrunch Registry