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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
https://github.com/dandi/dandi-cli/
Command line client to facilitate common operations.
Proper citation: dandi-cli (RRID:SCR_019009) Copy
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
Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install.
Proper citation: BioConda (RRID:SCR_018316) Copy
https://bio.tools/galactic_circos
Software tool as Galaxy wrapper providing GUI for Circos tool. Circos allows visualizing data in circular format.
Proper citation: Galactic Circos (RRID:SCR_018207) Copy
https://github.com/mridulaprasad/CorrDrugTumorMSI
Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data.
Proper citation: CorrDrugTumorMSI (RRID:SCR_018962) Copy
https://pypi.org/project/jupyter-client/5.2.3/
Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels.
Proper citation: Jupyter-client (RRID:SCR_018413) Copy
https://github.com/HMPNK/CSA2.6
Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.
Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy
https://github.com/jupyter/jupyter_console
Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal.
Proper citation: Jupyter-console (RRID:SCR_018414) Copy
https://nose.readthedocs.io/en/latest/
Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2.
Proper citation: Python Nose (RRID:SCR_018418) Copy
https://www.flidea.tech/flic-support
Software tool as user interface for running Fly Liquid Food Interaction Counter experiments.
Proper citation: FLIC Monitor (RRID:SCR_018387) Copy
http://bioconductor.org/packages/org.Rn.eg.db/
Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.
Proper citation: org.Rn.eg.db (RRID:SCR_018358) Copy
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
https://github.com/cobilab/geco3/
Software tool as DNA compressor that uses neural network to do mixing of experts.
Proper citation: GeCo3 (RRID:SCR_018877) Copy
Software tool for creating solid 3D CAD objects. Used for creating 3D models focusing on CAD aspects of 3D modeling of machine parts. Reads in script file that describes object and renders 3D model from this script file.
Proper citation: OpenSCAD (RRID:SCR_018870) Copy
Open source software application that enables services for online surveys. Provides advanced support for all steps of web survey process. Conduct research and analysis from beginning to end.
Proper citation: 1KA (RRID:SCR_019283) Copy
https://github.com/liqiwei2000/BayesEpiModels
Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework.
Proper citation: BayesEpiModels (RRID:SCR_019291) Copy
Software tool as free color blindness simulator for Windows, Mac and Linux. Design for Color Impaired. Takes guesswork out of designing for color blindness by showing you in real time what people with common color vision impairments will see.Color Oracle is open source, available on GitHub for Mac and Windows/Java.
Proper citation: Color Oracle (RRID:SCR_018400) Copy
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
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
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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