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https://lifesciencedb.jp/bp3d/
Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer.
Proper citation: Anatomography (RRID:SCR_018147) Copy
https://github.com/smortezah/smashpp
Software tool to find and visualize rearrangements in DNA sequences.
Proper citation: smashpp (RRID:SCR_018307) Copy
http://compbio.mit.edu/ChromHMM/
Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.
Proper citation: ChromHMM (RRID:SCR_018141) Copy
Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup.
Proper citation: GPS-SUMO (RRID:SCR_018261) Copy
https://biit.cs.ut.ee/gprofiler/page/r
Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.
Proper citation: gProfiler2 (RRID:SCR_018190) Copy
Stand alone software that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales. Successor of PhotoScan and is advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images.
Proper citation: Agisoft Metashape (RRID:SCR_018119) Copy
Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.
Proper citation: RaptorX (RRID:SCR_018118) Copy
Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction.
Proper citation: FlowPy (RRID:SCR_018195) Copy
https://www.kicnet.co.jp/solutions/biosignal/biosignal-2/vitalrecorder2/
Sleep recording software by Kissei Comtech Co., Ltd. Can measure signals of up to 32 channels while monitoring wave forms in real time. Addition of video recording option enables simultaneous recording of biological signals and video.
Proper citation: VitalRecorder2 (RRID:SCR_018199) Copy
https://www.fibl.org/en/themes/sustainability-assessment-info/sustainability-assessment-smart.html
Web and offline tool for holistic sustainability assessment of farms. Tool operationalizes Sustainability Assessment of Food and Agriculture Systems Guidelines of Food and Agriculture Organisation of United Nations. Tool consists of questionnaire software, centralized database, pool of indicators and scientifically based assessment methodology. Different stakeholders can use results of this assessment e.g. for comparing different farms, production systems or for strategic development, improvement, monitoring and communication to business partners.
Proper citation: SMART-Farm Tool (RRID:SCR_018197) Copy
http://ultrascan.aucsolutions.com/
Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.
Proper citation: UltraScan (RRID:SCR_018126) Copy
https://github.com/BGI-Qingdao/HAST
Software tool for partition stLFR reads based on trio binning using prenatally unique markers. Haplotype resolved assembly for synthetic long reads using Trio-Binning strategy.
Proper citation: HAST (RRID:SCR_018247) Copy
Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP.
Proper citation: CLIP-Explorer (RRID:SCR_018128) Copy
http://www.imperial.ac.uk/research/animallectins
Resource presents information about animal lectins involved in various sugar recognition processes.
Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy
Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest.
Proper citation: Stan (RRID:SCR_018459) Copy
Portal dedicated to funding lung cancer research by LUNGevity Foundation. Supports patient focused research and convene multi stakeholder meetings to streamline research process and accelerate progress to patients. Seeks to empower patients to be active decision makers in their treatment process through educational resources, online peer-to-peer support, and in-person survivorship programs.
Proper citation: LUNGevity (RRID:SCR_018570) Copy
Software tool to calculate ratio of intensity in nuclei and cytoplasm. It needs two images as input cytoplasm channel and nuclei channel.
Proper citation: Intensity Ratio Nuclei Cytoplasm Tool (RRID:SCR_018573) Copy
https://noblis.org/bioportal/tools.html
Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes.
Proper citation: BioVelocity (RRID:SCR_018501) Copy
https://www.ttuhsc.edu/pharmacy/research/documents/Amnis-Imagestream-Manual.pdf
Bench top multispectral imaging flow cytometer designed for the acquisition of up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry.
Proper citation: Luminex: Amnis ImageStreamX Mk II System (RRID:SCR_018589) Copy
http://www.nitrc.org/projects/reprocontainers/
Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.
Proper citation: ReproNim/containers (RRID:SCR_018467) Copy
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