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https://www.opensciencedatacloud.org/

Service that provides petabyte-scale cloud resources to analyze, manage, and share scientific data. It is designed to serve medium to large sized research projects by managing and operating a secure cloud computing infrastructure that can be shared across a project. This Science as a Service approach to research saves scientists and their funders valuable time and money. All of the software developed is open source and hosted on GitHub. The OSDC also has 1PB of public data in a wide variety of disciplines. The data sets can downloaded over the internet or high performance networks such as Internet2, as well as computed over directly on the OSDC.

Proper citation: Open Science Data Cloud (RRID:SCR_003523) Copy   

•   Source: SciCrunch Registry

http://www.sb.cs.cmu.edu/drem

The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations

Proper citation: Dynamic Regulatory Events Miner (RRID:SCR_003080) Copy   

•   Source: SciCrunch Registry

http://impactstory.org/

A web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile.

Proper citation: ImpactStory (RRID:SCR_002632) Copy   

•   Source: SciCrunch Registry

http://phenoscape.org/

Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions.

Proper citation: Phenoscape (RRID:SCR_003799) Copy   

•   Source: SciCrunch Registry

http://www.cs.cmu.edu/~jernst/stem/

The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Short Time-series Expression Miner (STEM) (RRID:SCR_005016) Copy   

•   Source: SciCrunch Registry

http://www.autopack.org/

An open-source general packing algorithm that packs 3D objects onto surfaces, into volumes, and around volumes. It provides a general architecture to allow various packing algorithms to interoperate efficiently in the same model. autoPack can incorporate any packing solution into its modular python program architecture, but is currently optimized to provide a novel solution to the loose packing problem which places objects of discrete size into place (compared to advancing front, popcorn, or other fast tight-packing solutions that allow objects to scale to arbitrary masses.) Most popular 3D software programs now contain robust physics engines based on Bullet that can separate small collections of overlapping objects or allow volumes to be filled by pouring shapes from generators, but these approaches fails for large complex systems and result in either overlapping geometry, crashed software, or non-random gradients. Most packing algorithms are designed to position objects as efficiently as possible, but autoPack allows the user to select from random loose packing to highly organized packing methods����??even to choose both methods at the same time. autoPack positions 3D geometries into, onto, and around volumes with minimal to zero overlap. autoPack mixes several packing approaches and procedural growth algorithms. autoPack can thus place objects with forces and constraints to allow a high degree of control ranging from completely random distributions to highly ordered structures. * zero to minimal overlaps depending on the method used * accuracy vs speed parameters selected by the user * zero edge effects * complete control, from fully random to fully ordered distributions * agent-based interaction, weighting, and collision control

Proper citation: Autopack (RRID:SCR_006830) Copy   

•   Source: SciCrunch Registry

https://github.com/wyp1125/MCScanx

Software toolkit for detection and evolutionary analysis of gene synteny and collinearity.

Proper citation: MCScanX (RRID:SCR_022067) Copy   

•   Source: SciCrunch Registry

http://scholarometer.indiana.edu/

Scholarometer (beta) is a social tool to facilitate citation analysis and help evaluate the impact of an author''s publications. It is a social (crowdsourcing) application that leverages the wisdom of the crowds. Scholarometer makes visualization of author and discipline networks available on the web site. It requires users to tag their queries with one or more discipline names, choosing from predefined ISI subject categories or arbitrary tags. This generates annotations that go into a database, which collects statistics about the various disciplines, such as average number of citations per paper, average number of papers per authors, etc. This data is publicly available. Scholarometer users can save the finding into formats appropriate for local reference management software (e.g., EndNote), or for social publication sharing systems (e.g., BibSonomy). Currently, our system supports the following export formats: BibTex (BIB), RefMan (RIS), EndNote (ENW), comma-separated values (CSV), tab-separated values (XLS), and BibJSON. Export data is dynamically generated in response to any filter, merge or delete actions performed by the user. Since Scholarometer is a browser extension that provides a smart interface for Google Scholar, it does not have the limitations of server based citation analysis tools that sit between the user and Google Scholar. At the same time Scholarometer is not an application, such as Publish or Perish, and therefore it is platform independent and runs on every system that supports the Firefox or the Chrome browser. Still, Scholarometer uses Google Scholar, which provides the most comprehensive source of citation data across the sciences and social sciences. Scholarometer provides a RESTful web API so that other developers can make use of our crowdsourced data. Select the method on the left panel to see corresponding documentation. The extension/add-on code is available in the Mozilla Firefox Add-ons and Google Chrome Extensions repositories. Additional server-side code is not available at this time.

Proper citation: Scholarometer (RRID:SCR_004279) Copy   

•   Source: SciCrunch Registry

https://www.dataone.org/

A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community.

Proper citation: DataONE (RRID:SCR_003999) Copy   

•   Source: SciCrunch Registry

https://prr.osu.edu/

National facility for permanent curatorial preservation of rock collections from Antarctica and Southern Ocean. Repository preserves existing rock/dredge/unconsolidated/terrestrial core/photo archive collections for research use. Database allows online requests for sample loans. Mapping tool combines existing PRR database with high resolution satellite images of Antarctica, REMA or USGS topographic layers. PRR created Polar Rock Boxes for educators who are teaching about Earth science and Antarctica. Each Polar Rock Box contains samples with binder full of teaching information about Earth science and Antarctica. These boxes are freely available as short loans to US schools.

Proper citation: Polar Rock Repository (RRID:SCR_002212) Copy   

•   Source: SciCrunch Registry

https://obofoundry.org/ontology/cl.html

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

Proper citation: Cell Type Ontology (RRID:SCR_004251) Copy   

•   Source: SciCrunch Registry

http://www.biomart.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.

Proper citation: BioMart Project (RRID:SCR_002987) Copy   

•   Source: SciCrunch Registry

https://www.proteinspire.org/MOPED/

An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions.

Proper citation: MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) Copy   

•   Source: SciCrunch Registry

http://www.antweb.org/

Database of images, specimen records, and natural history information on ants including Search Tools, Regional Lists, In Depth Information, Ant Image Comparison Tool, PDF Field Guides, Maps on AntWeb and Google Earth, and Ant Genera of the World Slideshow. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images. As of February of 2013, AntWeb has 97,814 ant images, of 23,272 specimens representing over 10,549 species. AntWeb provides tools for submitting images, specimen records, annotating species pages, and managing regional species lists. AntWeb contains information on the ant faunas of several areas in the Nearctic and Malagasy biogeographic regions, and global coverage of all ant genera. AntWeb provides tools for exploring the diversity and identification of ants (Hymenoptera: Formicidae). These tools have been developed to encourage the study of ants, to facilitate the use of ants in inventory and monitoring programs, and to provide ant taxonomists with access to images of type specimens. AntWeb illustrates the diversity of ants by providing information and high quality color images of many of the approximately 10,000 known species of ants. AntWeb currently focuses on the species of the Nearctic and Malagasy biogeographic regions, and the ant genera of the world. Over time, the site will grow to describe every species of ant known.

Proper citation: AntWeb (RRID:SCR_004851) Copy   

•   Source: SciCrunch Registry

http://crcns.org

Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.

Proper citation: CRCNS (RRID:SCR_005608) Copy   

•   Source: SciCrunch Registry

http://www.clairlib.org

A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries.

Proper citation: Clair library (RRID:SCR_007019) Copy   

•   Source: SciCrunch Registry

http://www.plantgdb.org/

Software tools and databases for plant genomics.

Proper citation: PlantGDB (RRID:SCR_013166) Copy   

•   Source: SciCrunch Registry

http://planteome.org

An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers.

Proper citation: Planteome (RRID:SCR_014411) Copy   

•   Source: SciCrunch Registry

http://research.bioinformatics.udel.edu/iptmnet/

A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies.

Proper citation: iPTMnet (RRID:SCR_014416) Copy   

•   Source: SciCrunch Registry

http://www.algalresourcescollection.com/

Supplier of algae strains that aims to be a resource to both the HAB research community and biotechnological applications. Researchers can order and deposit strains with the ARC.

Proper citation: Algal Resources Collection (RRID:SCR_014942) Copy   

•   Source: SciCrunch Registry