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http://anya.igsb.anl.gov/Geneways/GeneWays.html
System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.
Proper citation: GeneWays (RRID:SCR_000572) Copy
Provides distributed services from Universities of Connecticut, Georgia, and Wisconsin to democratize application of high-field NMR spectroscopy for applications in biomedicine, materials science, and chemistry. Multi-institution collaboration creating distributed research infrastructure for NMR applications including resource discovery, access to NMR spectrometers, ranging from bench top to ultra-high field, knowledgebases on best practices, and data archiving and sharing.
Proper citation: NSF Network for Advanced NMR (RRID:SCR_025092) Copy
https://fmug.amaral.northwestern.edu/
Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors. Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms.
Proper citation: Find My Understudied Genes (RRID:SCR_025047) Copy
https://github.com/bmvdgeijn/WASP/
Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.
Proper citation: WASP (RRID:SCR_025497) Copy
Database of downscaled paleoclimate outputs at 2.5 minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. Database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264–3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma). Set of historical climate layers (climate grids) with spatial resolution of about 2.5 min. These data can be used for mapping and spatial modelling in Geographic Information Systems (GIS) or other computer programs.
Proper citation: PaleoClim database (RRID:SCR_025657) Copy
Transcription factor target database. Platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments and target genes or transcripts across multiple organisms.
Proper citation: tTFtarget (RRID:SCR_025631) Copy
Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions.
Proper citation: Predictomes (RRID:SCR_026691) Copy
https://github.com/malonge/RagTag
Collection of software tools for scaffolding and improving modern genome assemblies. Reference-based scaffolder. Used for fast and flexible genome assembly scaffolding and improvement.
Proper citation: RagTag (RRID:SCR_027293) Copy
http://www.cebm.brown.edu/openmee/index.html
Open-source, cross-platform software for ecological and evolutionary meta-analysis.
Proper citation: OpenMEE (RRID:SCR_027300) Copy
https://github.com/SynapseWeb/PyReconstruct
Software successor to the Reconstruct annotation tool. PyReconstruct runs on all major operating systems, breaks through legacy RAM limitations, features intuitive and collaborative curation system, and employs flexible and dynamic approach to image registration. Used to analyze, display, and publish experimental or connectomics data. Suited for generating ground truth to implement in automated segmentation, outcomes of which can be returned to PyReconstruct for proofreading and quality control.
Proper citation: PyReconstruct (RRID:SCR_027562) Copy
https://github.com/nygctech/PySeq2500
Software tool to control Illumina HiSeq 2500 System. Open source Python code base and flow cell design that converts Illumina HiSeq 2500 instrument, comprising epifluorescence microscope with integrated fluidics, into open platform for programmable applications without need for specialized engineering or software development expertise.Enables non-specialists to develop and implement fluidics coupled imaging methods in benchtop system.
Proper citation: PySeq2500 (RRID:SCR_027678) Copy
https://www.ou.edu/structuralbiology/cobre-core-facilities/mcl
Offers access to instrumentation, training and services for structure determination of macromolecular molecules using single crystal X-ray diffraction and/or cryo-EM Single Particle Analysis (SPA). Instrumentation is available for initial crystallization trials, optimization of crystallization, single crystal X-ray diffraction and data collection at synchrotron radiation facilities, as well as electron microscopy grid preparation for cryo-EM (SPA), screening and data collection using a Thermo Scientific Tundra Cryo-TEM and assistance for data collection at national laboratories.
Proper citation: University of Oklahoma Biomolecular Structure Core Facility (RRID:SCR_028074) Copy
https://dnarepair.bas.bg/software/CellTool/
Stand-alone open-source software with graphical user interface for analysis of time-lapse microscopy images. Combines bio-image analysis and mathematical modeling for study of DNA repair dynamics.
Proper citation: CellTool (RRID:SCR_028232) Copy
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