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https://github.com/nlm-irp-jianglab/SpikeHunter
Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins.
Proper citation: SpikeHunter (RRID:SCR_024831) Copy
https://github.com/xinhe-lab/GSFA
Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.
Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links.
Proper citation: Academic Seismic Portal at UTIG (RRID:SCR_000403) Copy
http://cbl.uh.edu/ORION/research/software
ORION is our neuron reconstruction software package developed for the morphological reconstruction of neurons from confocal and multiphoton microscopy data. It accepts raw neuron stack data as input and it is capable of reconstructing the neuron structure, visualizing the output, and exporting the reconstruction in a variety of formats. We are developing tools that will enable Neuroscientists to explore single neuron function via sophisticated image analysis. Advanced optical imaging can produce both structural and functional data and is at the forefront of experimentally exploring the fast, small-scale dynamics of living neurons. Further, compartmental modeling of neuronal function enables rapid testing of hypotheses and estimating experimentally inaccessible parameters. Combining these two techniques will afford unprecedented capabilities in the study of single neuron function. Our software utility bridges the two Neuroscience techniques by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.
Proper citation: ORION Software (RRID:SCR_004389) Copy
http://www.scrible.com/#desktop
We''re bringing Web-based research into the Internet Era by empowering people to mark up web pages in the browser and manage and collaborate on them online. And that''s just the start... We''ve got much more planned in a variety of areas to help people manage the mounds of info they''re pulling off the Web everyday. Simply drag the scrible bookmarklet to your browser''s Bookmarks toolbar. Click it later to mark up, save or share web pages. Even though the world uses the Internet to research nearly everything for work, school and home (job postings, press releases, Wikipedia articles, medical info, etc.), most folks still use old-school ways of annotating, organizing and sharing online info (printing to mark by hand, copying/pasting into Word, etc.). It''s archaic, laborious and a waste of time. We''re changing that. A bookmarklet is a bookmarked link that, when clicked, adds functionality to your browser. When the scrible Bookmarklet is clicked, it loads the scrible Toolbar atop the current webpage you''re viewing. Adding the scrible Bookmarklet to your browser is a breeze. Simply drag it to your browser''s Bookmarks Toolbar.
Proper citation: scrible (RRID:SCR_008882) Copy
https://pynwb.readthedocs.io/en/latest/
Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.
Proper citation: PyNWB (RRID:SCR_017452) Copy
https://github.com/compbiolabucf/omicsGAN
Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.
Proper citation: OmicsGAN (RRID:SCR_022976) Copy
Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils.
Proper citation: rockd (RRID:SCR_024431) Copy
https://www.danforthcenter.org/our-work/core-facilities/advanced-bioimaging-laboratory/
Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff.
Proper citation: Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility (RRID:SCR_018951) Copy
https://www.colorado.edu/rc/resources/petalibrary
Provides service to support storage, archival, and sharing of research data. Available at subsidized cost to any researcher affiliated with University of Colorado Boulder.
Proper citation: University of Colorado Boulder High Performance Computing PetaLibrary Core Facility (RRID:SCR_019299) Copy
https://www.jmu.edu/microscopy/index.shtml
Core provides instrumentation, resources, training, and consultation. Facility offers access to diverse range of light microscope and imaging systems,image analysis software and solutions, practical and theoretical training for faculty, students and classes,consultation on data acquisition, analysis, and presentation.
Proper citation: James Madison University Light Microscopy and Imaging Core Facility (RRID:SCR_021904) Copy
T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.
Proper citation: T-REX (RRID:SCR_010715) Copy
A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.
Proper citation: CRAVAT (RRID:SCR_012776) Copy
http://www.collectf.org/browse/home/
A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements.
Proper citation: CollecTF (RRID:SCR_014405) Copy
A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others.
Proper citation: Mouse Phylogeny Viewer (RRID:SCR_014071) Copy
Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.
Proper citation: CIS-BP (RRID:SCR_017236) Copy
https://www.umass.edu/ials/pccl-database
Collection of plant species for use by both academia and industry.The PCCL enables R&D exploitation of monocot, dicot and gymnosperm cultures.
Proper citation: Plant Cell Culture Library (PCCL) (RRID:SCR_016784) Copy
http://www.biocheminfo.org/klotho/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry.
Proper citation: Klotho: Biochemical Compounds Declarative Database (RRID:SCR_007714) Copy
http://www3.isrl.uiuc.edu/~TeleNature/bibe/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A facility to help novices and experts find information about plants and animals in digital collections. The objectives of the Project are to facilitate access to online flora and fauna by both novices and experts through enhanced indexing, searching, and visualization techniques. Specific search facility and content will be added to help users with different levels of domain knowledge identify species based on the augmentation of professionally developed taxonomic treatments or species descriptions. This is a novel use of taxonomic descriptions.
Proper citation: Biological Information Browsing Environment (RRID:SCR_008170) Copy
Provides genomics and molecular biology services for University of Delaware research groups and outside users.Supports genomic research through established expertise with genomics technologies.
Proper citation: University of Delaware Sequencing and Genotyping Center Core Facility (RRID:SCR_012230) Copy
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