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http://purl.bioontology.org/ontology/MAMO

Ontology that is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.

Proper citation: Mathematical Modelling Ontology (RRID:SCR_000910) Copy   

•   Source: SciCrunch Registry
  

https://microbiomedata.org

Platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science. Multi organizational effort to integrate microbiome data across diverse areas in medicine, agriculture, bioenergy, and environment. Founded to support long term advancement of microbiome science.

Proper citation: National Microbiome Data Collaborative (RRID:SCR_022161) Copy   

•   Source: SciCrunch Registry
  

https://osf.io/xfpn4/

MDAR Framework establishes minimum set of requirements in transparent reporting applicable to studies in life sciences. MDAR checklist is tool for authors, editors and others seeking to adopt MDAR framework for transparent reporting in manuscripts and other outputs and designed to provide harmonizing principle for reporting requirements currently in use at various journals.

Proper citation: MDAR (RRID:SCR_022038) Copy   

•   Source: SciCrunch Registry
  

https://elucidata.io/el-maven/

Open source LC-MS data processing engine for simplifying metabolomics analysis. Mass spectrometry data processing engine that is optimal for isotopomer labeling and global metabolomic profiling experiments. Interactive software platform that accelerates analysis of LC-MS, GC-MS, and LC-MS/MS datasets.

Proper citation: EL MAVEN (RRID:SCR_022159) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/granulator.html

Software R package for cell type deconvolution of heterogeneous tissues based on bulk RNAseq data or single cell RNAseq expression profiles.Provides unified testing interface to rapidly run and benchmark multiple deconvolution methods.

Proper citation: granulator (RRID:SCR_022158) Copy   

•   Source: SciCrunch Registry
  

http://www.khri.med.umich.edu/research/lesperance_lab/low_freq.php

This web site lists the disease causing mutations and polymorphisms found in the Wolfram syndrome (WFS1) gene. Sponsors: This resource is supported by the University of Michigan at Ann Arbor.

Proper citation: Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database (RRID:SCR_001113) Copy   

•   Source: SciCrunch Registry
  

https://github.com/mourisl/Rcorrector

Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads.

Proper citation: Rcorrector (RRID:SCR_022011) Copy   

•   Source: SciCrunch Registry
  

https://pna.creative-peptides.com/services/synthesis-by-fmoc-chemistry.html

Provides Fmoc based PNA synthesis. Route consists of repeated cycles of deprotection, activation, coupling and capping.Synthesis of small scale PNA oligomers, which can be performed on common DNA synthesis platforms.

Proper citation: Creative Peptides Chemical Synthesis of PNA Oligomers with Fmoc Service Resource (RRID:SCR_022132) Copy   

•   Source: SciCrunch Registry
  

https://www.bcgsc.ca/resources/software/ntcard

Software tool for estimating k-mer coverage histogram of genomics data. Streaming algorithm for estimating frequencies of k-mers in genomics datasets.

Proper citation: ntCard (RRID:SCR_022010) Copy   

•   Source: SciCrunch Registry
  

http://www.frontiersin.org/10.3389/conf.fninf.2013.09.00111/event_abstract

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. ASP.NET AJAX .NET 4, Telerik controls enabled application designed to be used with the books presented, papers and web content to help with the acceleration of learning and software development for the neurosciences. All content developed at The Cromwell Workshop is intended to accelerate the implementation of biomedical knowledge, help with EEG clinical certifications and provide the opportunity for students, software developers, neuroscientists, neurologists and neurosurgeons to collaborate globally with knowledge content. e-NeoTutor relies on a subscription model to build software components in multiple languages and access book material. Tutor designed to complement free online course content in neuroscience, work with the Society of Neuroscience, The Human Connectome Project and assist researchers with CNIM certification, biomedical informatics, neuroinformatics and neuroscience training programs.

Proper citation: eNeoTutor (RRID:SCR_001590) Copy   

•   Source: SciCrunch Registry
  

http://connect-tbi.med.upenn.edu/

Portal for traumatic brain injury data. Common Data Elements (CDEs) and Unique Data Elements (UDEs) for digital neuropathological data and clinical data that will be collected in all CONNECT-TBI center projects. Goal is to establish multi-center, digital neuropathological data and clinical data reporting network with case accrual from each center project. Collected neuropathological data and clinical data available by sharing with center site investigators approved by Administrative Core and by submitting into FITBIR. Central TBI data repository by collecting digital neuropathological data and clinical data from TBI cases and normal controls at each center and posting library of their holdings.

Proper citation: Connect TBI (RRID:SCR_022009) Copy   

•   Source: SciCrunch Registry
  

https://rubyonrails.org/

Open source web application development framework. Model View Controller framework, providing default structures for database, web service, and web pages.

Proper citation: Ruby on Rails (RRID:SCR_022129) Copy   

•   Source: SciCrunch Registry
  

https://github.com/neuronanalyser/neuronanalyser

Software analysis toolkit for tracking blobs and extracting intensity values from imaging data, designed for use with ratiometric fluorescent sensors.

Proper citation: Neuronanalyser (RRID:SCR_022007) Copy   

•   Source: SciCrunch Registry
  

https://www.plumed.org/

Open source, community developed library that provides range of different methods, which include enhanced sampling algorithms, free energy methods, tools to analyze vast amounts of data produced by molecular dynamics simulations. PLUMED 2 is complete rewrite of the code in object oriented programming language C plus plus. This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has simpler interface with the MD engines and provides single software library containing both tools and core facilities.

Proper citation: PLUMED 2 (RRID:SCR_021952) Copy   

•   Source: SciCrunch Registry
  

https://ptc.bocsci.com/services/protein-ubiquitination-services.html

Service in field of drug discovery and research. BOC Sciences service in one stop Proteolysis Targeting Chimeric based molecular drug discovery which has become strategy in area of drug discovery.

Proper citation: BOC Sciences Protein Ubiquitination Service Resource (RRID:SCR_022127) Copy   

•   Source: SciCrunch Registry
  

https://ptc.bocsci.com/services/small-molecule-target-protein-ligand.html

Provides small molecule target protein ligand service to customers to meet new drug discovery goals.

Proper citation: BOC Sciences Small molecule target protein ligand Service Resource (RRID:SCR_022126) Copy   

•   Source: SciCrunch Registry
  

https://ptc.bocsci.com/services/peptide-ligand-for-target-protein.html

Service provider in drug discovery and development. Provides one stop PROTA development, which has become strategy in field of small molecular drug discovery. Provides peptide ligand design for target protein to customers to meet new drug discovery goals.

Proper citation: BOC Sciences Peptide ligand for target protein Service Resource (RRID:SCR_022125) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/package=StAMPP

Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels.

Proper citation: StAMPP (RRID:SCR_022022) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/package=hierfstat

Software R package for estimation and tests of hierarchical F statistics.Used to estimate hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in hierarchy.Intended for analysis of population structure using genetic markers.

Proper citation: hierfstat (RRID:SCR_022021) Copy   

•   Source: SciCrunch Registry
  

http://coins.mrn.org/

A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS.

Proper citation: Mind Research Network - COINS (RRID:SCR_000805) Copy   

•   Source: SciCrunch Registry