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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://www.kbdna.com/

Commercial provider of antibodies, antigens and recombinant proteins from Braintree, Massachusetts . Biotechnology company which provides custom oligonucleotides synthesis service.

Proper citation: kbDNA Inc. (RRID:SCR_016570) 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://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

http://www.getpaint.net/

Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools.

Proper citation: paint.net (RRID:SCR_017641) Copy   

•   Source: SciCrunch Registry

https://github.com/pachterlab/kb_python

Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).

Proper citation: kb_python (RRID:SCR_018213) Copy   

•   Source: SciCrunch Registry

http://treesoft.sourceforge.net/treebest.shtml

Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate.

Proper citation: TreeBeST (RRID:SCR_018173) 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://github.com/smajidian/phaseme

Software tool set to assess quality of per read phasing information and help to reduce errors during this process.

Proper citation: PhaseME (RRID:SCR_018739) 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://www.biorxiv.org/content/10.1101/2020.09.24.311282v2.full

Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape.

Proper citation: QuickFigures (RRID:SCR_019082) Copy   

•   Source: SciCrunch Registry

http://www.perl.org

Software tool to accompany existing resources such as Python programming language resource and comprehensive Perl archive network (CPAN) resource. Perl is family of two high level, general purpose, interpreted, dynamic programming languages. Perl refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned sister language, Perl 6, before name was officially changed to Raku in October 2019.

Proper citation: Perl Programming Language (RRID:SCR_018313) Copy   

•   Source: SciCrunch Registry

https://www.rankinbiomed.com/product/refurbished-american-optical-860-sliding-micrtome/

THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns.

Proper citation: American Optical: 860 Sliding Microtome (RRID:SCR_018434) 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://github.com/NuttyLogic/EpigeneticPacemaker

Python implementation of conditional expectation maximization algorithm that estimates epigenetic landscapes and state of individuals and may be used to study nonlinear epigenetic aging. Fast conditional expectation maximization algorithm used to model epigenetic states associated with phenotype of interest. Can model non linear epigenetic trait associations directly without transformation of phenotype of interest.

Proper citation: Epigenetic Pacemaker (RRID:SCR_018158) Copy   

•   Source: SciCrunch Registry

https://atagousa.corecommerce.com/PAL-10S-p358.html

Digital hand held pocket refractometer that measures urine specific gravity. It has measurement temperature of 10 to 35 C and sample volume of 0.3ml.

Proper citation: Atago: PAL-10S Pocket Refractometer (RRID:SCR_018439) Copy   

•   Source: SciCrunch Registry

https://docs.conda.io/en/latest/

Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda.

Proper citation: Conda (RRID:SCR_018317) Copy   

•   Source: SciCrunch Registry