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http://www.salk.edu/science/core-facilities/media-preparation-core/

Core facility that provides media, plates, and commonly used buffers for molecular biology applications and culturing mammalian cells, C. elegans, yeast, and bacteria. The Media Preparation Core Facility is equipped with 3 automatic plate pourers supported by 2 programmable media kettles capable of producing up to 9 liters of agar or nutrient media per run under gentle and reproducible conditions. Plates are available in 6 cm or 10 cm formats.

Proper citation: Salk Institute Media Preparation Core Facility (MPRP) (RRID:SCR_014844) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/

Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects.

Proper citation: OpenBehavior (RRID:SCR_015938) Copy   

•   Source: SciCrunch Registry
  

https://CRAN.R-project.org/package=Boruta

Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).

Proper citation: Boruta (RRID:SCR_016234) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/MIIVsem/index.html

Software R package for estimating structural equation models using instrumental variables.

Proper citation: MIIVsem (RRID:SCR_017444) Copy   

•   Source: SciCrunch Registry
  

https://www.lenntech.com/calculators/activity/activity-coefficient.htm

Software tool to calculate the activity coefficient of an ion in solution by Lenntech B.V. Determines the ionic strength of solution by using the concentration of ions present in drinking water.

Proper citation: Lenntech activity coefficient calculator (RRID:SCR_016475) Copy   

•   Source: SciCrunch Registry
  

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_StemCells.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) Copy   

•   Source: SciCrunch Registry
  

https://github.com/QTIM-Lab/DeepNeuro

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.

Proper citation: DeepNeuro (RRID:SCR_016911) Copy   

•   Source: SciCrunch Registry
  

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_TumorAnalysis.aspx

Facility that provides analysis of animal models of human cancer and other diseases. It provides investigators access to a wide variety of human cancer cell lines for xenograft studies, some primary human xenograft models and additional transgenic mouse solid tumors and leukemia models. The core also offers serial passaging of tumors and derivation of 2D and 3D cultures from xenograft tumors, including patient-derived xenograft (PDX) models. These short-term cell cultures established from PDXs enable in vitro analysis including high throughput screening with compounds or RNAi for functional characterization.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Tumor Analysis (RRID:SCR_014858) Copy   

•   Source: SciCrunch Registry
  

http://rkscope.sourceforge.net/

Two photon microscope control software with multi area capabilities.

Proper citation: Scope (RRID:SCR_017454) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vlchaplin/pyRayleighCuda

Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation.

Proper citation: pyRayleighCuda (RRID:SCR_017453) Copy   

•   Source: SciCrunch Registry
  

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

Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.

Proper citation: PyNWB (RRID:SCR_017452) Copy   

•   Source: SciCrunch Registry
  

https://github.com/bio2bel

Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications.

Proper citation: Bio2BEL (RRID:SCR_017659) Copy   

•   Source: SciCrunch Registry
  

http://download.ant-neuro.com/matlab/

Software as an EEGLAB tool used for LIBEEP recordings.

Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy   

•   Source: SciCrunch Registry
  

http://www.nikon.com/products/microscope-solutions/support/download/software/confocal/c1_freevw_v390.htm

Software for browsing the image data acquired by Nikon C1 and a Nikon C1si system.

Proper citation: EZ-C1 FreeViewer (RRID:SCR_014277) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html

Software package which brings to R color scales. Created for the Python matplotlib library.

Proper citation: viridis (RRID:SCR_016696) Copy   

•   Source: SciCrunch Registry
  

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
  

http://www.rdkit.org/

An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website.

Proper citation: RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) Copy   

•   Source: SciCrunch Registry
  

http://www.vet.upenn.edu/research/core-resources-facilities/referral-center-for-animal-models

Center that aims to discover, characterize, maintain breeding colonies, and make available dog and cat models with hereditary diseases homologous to those found in human patients that can be used to translate preclinical trials from kennel to clinic. The animal models represent true orthologs of their respective human disease, involving defects in homologous genes resulting in similar molecular, biochemical, pathological, and clinical phenotype as in human patients.

Proper citation: Referral Center for Animal Models of Human Genetic Diseases (RRID:SCR_016453) 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