Tools   Select Another Resource Report Type

http://gila.bioengr.uic.edu/snp/toposnp

A topographic database for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins. These include disease- associated nsSNPs derived from the Online Mendelian Inheritance in Man (OMIM) database and other nsSNPs derived from dbSNP, a resource at the National Center for Biotechnology Information that catalogs SNPs. TopoSNP further classifies each nsSNP site into three categories based on their geometric location: those located in a surface pocket or an interior void of the protein, those on a convex region or a shallow depressed region, and those that are completely buried in the interior of the protein structure. These unique geometric descriptions provide more detailed mapping of nsSNPs to protein structures. It also includes relative entropy of SNPs calculated from multiple sequence alignment as obtained from the Pfam database (a database of protein families and conserved protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW. These structural and conservational data can be useful for studying whether nsSNPs in coding regions are likely to lead to phenotypic changes. TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data.

Proper citation: TopoSNP (RRID:SCR_005572) Copy   

•   Source: SciCrunch Registry

http://www.bindingdb.org

Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs .

Proper citation: BindingDB (RRID:SCR_000390) Copy   

•   Source: SciCrunch Registry

http://www.data.scec.org/

Archive of earthquake data for research in seismology and earthquake engineering in Southern California recorded or processed by the Southern California Seismic Network (SCSN). Users can access information on: * Recent earthquakes detected by the SCSN * Significant southern California earthquakes and faults * The southern California earthquake catalog, spanning from 1933 to present * Waveform and metadata files of SCSN seismic stations from 1977 to present * Data sets created by SCEC scientists to assist in ongoing and future research

Proper citation: Southern California Earthquake Data Center (RRID:SCR_000663) Copy   

•   Source: SciCrunch Registry

http://criticalzone.org/

Data related to the National Critical Zone Observatory Program including in-situ environmental sensors, field instruments, remote sensing, and surface and subsurface imaging. The Program serves the international scientific community through research, infrastructure, data, and models. They focus on how components of the Critical Zone interact, shape Earth's surface, and support life. A primary goal is to develop high-resolution 4D datasets that inform our theoretical framework, constrain our conceptual and coupled systems models, and test our model-generated hypotheses. They are developing cross-CZO capabilities to easily share, integrate, analyze and preserve the wide range of multi-disciplinary data generated by CZOs.

Proper citation: Critical Zone Observatories (RRID:SCR_002199) Copy   

•   Source: SciCrunch Registry

http://www.marine-geo.org/portals/seismic/

Seismic Reflection Field Data from the academic research community. Their partner Academic Seismic Portal at UTIG offers additional seismic resources, http://www.ig.utexas.edu/sdc/

Proper citation: Academic Seismic Portal at LDEO (RRID:SCR_002194) Copy   

•   Source: SciCrunch Registry

http://www.ornisnet.org/

ORNIS is a database of bird specimens as well as a portal to connect the academic and museum communities involved with studying birds. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Over 5 million bird specimens are housed in North American collections, documenting the composition, distribution, ecology, and systematics of the world's estimated 10,000-16,000 bird species. Millions of additional observational records are held in diverse data sets. ORNIS addresses the urgent call for increased access to these data in an open and collaborative manner, and involves development of a suite of online software tools for data analysis and error-checking. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Improved access to avian data sets will allow predictive uses to reveal patterns and processes of evolutionary and ecological phenomena that have not been apparent heretofore. Along with similar infrastructures for other vertebrate groups, it also will enable detailed and synthetic knowledge of the earth's biodiversity for tracking climate change, emerging diseases (e.g., West Nile Virus), and other conservation challenges for species in the 21st century.

Proper citation: ORNIS (RRID:SCR_002896) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/db/Search

Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Proper citation: Genes to Cognition Database (RRID:SCR_002735) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_FINDER_parallel

Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.

Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy   

•   Source: SciCrunch Registry

https://opensciencechain.org/

Provides data integrity using blockchain. Used for protecting integrity and provenance of research data.Open science chain utilizes distributed ledger technology (consortium blockchain) to securely store information about scientific data including its provenance to enable independent verification of its authenticity to establish trust in the research community.

Proper citation: Open Science Chain (RRID:SCR_018773) Copy   

•   Source: SciCrunch Registry

http://scratch.proteomics.ics.uci.edu/

Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors.

Proper citation: ANTIGENpro (RRID:SCR_018779) Copy   

•   Source: SciCrunch Registry

https://github.com/KarrLab/de_sim

Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models.

Proper citation: DE-Sim (RRID:SCR_018770) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@[email protected]

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

https://brainlife.io/

Free cloud platform for secure neuroscience data analysis. Allows to manage data, processing and results, sharing projects privately with collaborators or publicly with brainlife.io community.Promotes engagement and education in reproducible neuroscience.You can share your neuroimaging data publicly or privately. Data on brainlife.io is organized as Datatypes to allow interoperability between Apps.

Proper citation: brainlife (RRID:SCR_020940) Copy   

•   Source: SciCrunch Registry

https://nanohub.org

A portal which provides simulation programs for nanoscale phenomena, online presentations, courses, learning modules, podcasts, animations, and teaching materials. Researchers can also collaborate with others and publish content.

Proper citation: nanoHUB (RRID:SCR_013963) Copy   

•   Source: SciCrunch Registry

https://github.com/CBL-ORION/orion

Project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION (RRID:SCR_010621) Copy   

•   Source: SciCrunch Registry

https://wholetale.org/

Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.

Proper citation: Whole Tale (RRID:SCR_017537) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_retriever

Software package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly.

Proper citation: LTR_retriever (RRID:SCR_017623) Copy   

•   Source: SciCrunch Registry

https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

•   Source: SciCrunch Registry

https://github.com/Cai-Lab-at-University-of-Michigan/nTracer

Software tool as plug-in for ImageJ software. Used for tracing microscopic images.

Proper citation: nTracer (RRID:SCR_023032) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/APA-Scan

Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.

Proper citation: APA-Scan (RRID:SCR_022974) Copy   

•   Source: SciCrunch Registry