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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
https://zenodo.org/records/11095105
Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification.
Proper citation: SIMS (RRID:SCR_025787) 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/slowkoni/rfmix
Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference.
Proper citation: RFMix (RRID:SCR_027030) 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://github.com/TonnesenLab/Diffusion-Model/
Software code for simulating diffusion in brain extracellular space images.
Proper citation: Diffusion-Model (RRID:SCR_027942) 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
Spectrometer represents the pinnacle of commercial nuclear magnetic resonance technology. Operating at 28.2 Tesla, this ultra-high-field system is primarily used for advanced structural biology, pharmaceutical research, and materials science. Delivers the highest commercially available spectral resolution, crucial for investigating complex protein dynamics, functional molecular disorders, and viral structures. Console:Avance Neo; Magnet:Gateway; Field Strength: 1.2 GHz; Software:TopSpin 4.4.1 on CentOS 7; Probes:3mm TCI cryoprobe; 3mm BBI room-temperature; 3.2mm HX low-gamma MAS; 1.9mm HX high-gamma MAS; 1.3mm HCN fast MAS; 0.7mm HCN ultra-fast MAS; Chilled SampleCase (up to 24 samples); Automated Tuning and Matching (ATM); Nitrogen Liquefier.
Proper citation: Bruker: Avance Neo 1.2 GHz NMR Spectrometer (RRID:SCR_028512) Copy
https://cells-test.gi.ucsc.edu/cytoverse/
Web application to map single-cell RNA data into AI foundation model spaces. Lets search millions of reference cells and view cell types locally without uploading private data or needing powerful cloud servers. Using ONNX model deployment and compressed IVFPQ indexing, it annotates local datasets against a 23-million-cell reference without server computation, installation, or data upload, and shares embeddings as lightweight files, enabling private, interactive, and collaborative single-cell analysis.
Proper citation: CytoVerse (RRID:SCR_028854) Copy
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