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https://github.com/Kingsford-Group/kourami

Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.

Proper citation: Kourami (RRID:SCR_022280) Copy   

•   Source: SciCrunch Registry
  

https://opencell.czbiohub.org/

Proteome scale collection of protein localization and interaction measurements in human cells. Proteome scale endogenous tagging enables cartography of human cellular organization.

Proper citation: OpenCell (RRID:SCR_021870) Copy   

•   Source: SciCrunch Registry
  

https://isamplesorg.github.io/home/

Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications.

Proper citation: iSamples (RRID:SCR_021750) Copy   

•   Source: SciCrunch Registry
  

https://github.com/RabadanLab/arcasHLA

Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq.

Proper citation: arcasHLA (RRID:SCR_022286) Copy   

•   Source: SciCrunch Registry
  

https://www.kbase.us/

Data science platform for predicting and designing biological function. Platform to model plant and microbial physiology and community dynamics. Knowledge creation and discovery environment for biologists and bioinformaticians. Integrates variety of data and analysis tools from US Department of Energy and other public services into platform that leverages scalable computing infrastructure and performs systems biology analyses. Enables scientists to analyze their own data within context of public data and share findings across system.

Proper citation: KBase (RRID:SCR_022162) Copy   

•   Source: SciCrunch Registry
  

https://ccsp.hms.harvard.edu/

Center includes studies for responsiveness and resistance to anti cancer drugs. Committed to training students and postdocs, promoting junior faculty and ensuring that data and software are reproducible, reliable and publicly accessible. Member of National Cancer Institute’s Cancer Systems Biology Consortium.

Proper citation: Harvard Medical School Center for Cancer Systems Pharmacology (RRID:SCR_022831) Copy   

•   Source: SciCrunch Registry
  

https://www.turing.ac.uk/research/research-projects/turing-way-handbook-reproducible-data-science

Guide to reproducible data science to support students and academics as they develop their code, with aim of helping them produce work that will be regarded as gold standard examples of trustworthy and reusable research. Include training material on version control, analysis testing and open and transparent communication with future users.

Proper citation: Turing Way handbook for reproducible data science (RRID:SCR_021908) Copy   

•   Source: SciCrunch Registry
  

https://bcrj.org.br/

Collection as result of joint work of scientists, technicians and students from Federal University of Rio de Janeiro and Technical-Scientific Association Paul Ehrlich. Center of reference and excellence in cell culture in Brazil and in our continent. Collection of human and animal cells that operates as service provider in Brazil and is the largest in South America.

Proper citation: Rio de Janeiro Cell Bank (RRID:SCR_023181) Copy   

•   Source: SciCrunch Registry
  

https://catalog.bcrc.firdi.org.tw/

Systematic and service oriented BioResource Center in Asia. Member of World Federation for Culture Collections from 1984 until now. BCRC is the first BRC certified by international organization of ISO quality system. Approved by Taiwan Biodiversity Information Facility.

Proper citation: Taiwan Bioresource Collection and Research Center (RRID:SCR_023180) Copy   

•   Source: SciCrunch Registry
  

https://github.com/mourisl/Rascaf

Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data.

Proper citation: Rascaf (RRID:SCR_022014) Copy   

•   Source: SciCrunch Registry
  

https://finngen.gitbook.io/documentation/

Public private partnership combining genotype data from Finnish biobanks and digital health record data from Finnish health registries. Provides opportunity to study genetic variation in relation to disease trajectories in isolated population.

Proper citation: FinnGen (RRID:SCR_022254) Copy   

•   Source: SciCrunch Registry
  

http://kcb.kiz.cas.cn/ml/

Cell Bank provides high quality resources and services including cell lines/tissues/DNA samples; cell culture training/trouble-shooting; cell culture/genetic research equipment; cell line karyotype analysis; STR/mycoplasma contamination detection; chromosome painting; cell line preservation.Cell Bank is branch of National Platform of Experimental Cell Resources for Science and Technology, Wildlife Resource Bank of the Chinese Academy of Sciences, the China Germplasm Bank of Wild Species, and also affiliated with Institute’s State Key Laboratory of Genetic Resources and Evolution.

Proper citation: Kunming Wild Animal Cell Bank (RRID:SCR_023188) Copy   

•   Source: SciCrunch Registry
  

https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification

Software package as collection template and associated materials for SARS-CoV-2 metadata. Contains metadata collection template based on data standard designed to harmonize genomic surveillance contextual data (sample metadata, epidemiological/clinical/laboratory data, methods information) across datasets, laboratories and databases during pandemic, and beyond. Template contains standardized fields, terms and formats for structuring information, and is accompanied by field level reference guide which provides definitions, guidance and examples for populating fields. Fields have been prioritized using colour coding system as required (yellow), recommended (purple), and optional (white). Users can use as much or as little of specification as they wish, according to their needs, and need not share information unless permitted to do so. SOP and protocols for submitting to public repositories are also included.

Proper citation: Public Health Alliance for Genomic Epidemiology SARS-CoV-2 Contextual Data Specification (RRID:SCR_021378) Copy   

•   Source: SciCrunch Registry
  

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

Portable behavioural set up that incorporates both gait analysis (using pedobarograph) and whisker movements (using high speed video camera and infrared light source).Automatically records both whisker and gait information and provides added statistical tools to analyse data. LocoWhisk system includes ARTv2 software for simultaneous measurement of locomotion behaviours and whisker movements.

Proper citation: LocoWhisk project (RRID:SCR_021430) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/facesync/, https://bio.tools/FaceSync

Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.

Proper citation: FaceSync project (RRID:SCR_021393) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/head-fixed-setup-combined-behavior-electrophysiology-optogenetics/

Project related to temporally controlled rodent behavior. Provides system which utilizes optimal open source setup of hardware and software through behavioral setup for temporally controlled rodent behavior. Used for combined behavior, electrophysiology and optogenetics experiments. System allows for training of head fixed animals with calibrated sound stimuli, precisely timed fluid and air puff presentations as reinforcers.Combines microcontroller based behavior control with sound delivery system for acoustic stimuli, fast solenoid valves for reinforcement delivery and custom built sound attenuated chamber.

Proper citation: Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project (RRID:SCR_021427) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/kinemouse-wheel/

Project is related to Columbia University designed KineMouse Wheel, light weight running wheel for head fixed locomotion that allows for 3D positioning of mice with single camera. System uses single camera and DeepLabCut (or similar) software.

Proper citation: KineMouse Wheel project (RRID:SCR_021425) Copy   

•   Source: SciCrunch Registry
  

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

Project related to capturing detailed behavior in freely moving mice. System combines lightweight head mounted camera and head movement sensors to detect behaviors in mice. Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity.Provides software Python package with functions for extracting and analyzing data recorded using camera.

Proper citation: Mousecam project (RRID:SCR_021422) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/cap-touch-sensor/

Project related to accurately counting and monitoring the behavior of organisms.Provides open source capacitive touch sensing system.Capacitive sensors are positioned to readily detect direct physical touches from rodent under investigation. Device,designed around capacitive touch sensor MPR121,accurately counts and monitors behavior of organisms.

Proper citation: Capactive Touch Sensor project (RRID:SCR_021486) Copy   

•   Source: SciCrunch Registry
  

https://github.com/slundberg/shap

Software tool as unified framework for interpreting predictions of machine learning models. Used to explain output of any machine learning model. Connects optimal credit allocation with local explanations using classic Shapley values from game theory and their related extensions.

Proper citation: SHapley Additive ExPlanations (RRID:SCR_021362) Copy   

•   Source: SciCrunch Registry