Curator Dashboard

MATLAB software tool collection for data acquisition and image analysis from zero mode waveguides.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format).

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Genome tool for analyzing and annotating large genomic sequences containing introns. It includes a program for comparing the query sequence with a protein database and another for comparing the query with a cDNA database. The database search program identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence, as well as reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Genome sequence classification tool based on kmer. The code allows users to build nucleotide databases and protein databases, classify reads, construct binner databases, and create taxonomic relationship files. The website provides information on how to perform these actions with code, though users can access a web-based Taxonomer if they need/want to.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Tool for the classification of known transposable elements in eukaryotic genomes. It can be combined with ab initio repeat finding in order to recover contrasting transposable element landscapes between species.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Spike detection algorithm that is improvement to native spike detection algorithm of Wave_clus spike sorting software. Software patch that incorporates Taller Peaks algorithm into Wave_clus as optional spike detection algorithm for single wire data.

• Resource
• SciCrunch
• 10 years ago - by Anonymous

Web tool used to generate confidence scored and functionally annotated human protein-protein interaction networks. Users can run a protein query using a UniProt identifier (ID or accession), gene symbol or Entrez gene id, or a network query using set fields.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols.

• Resource
• NIF
• 10 years ago - submitted by Maryann Martone

NIH network designed to follow and help conduct clinical trials and research studies investigating acute stroke treatment, stroke prevention, and stroke recovery and rehabilitation. Clinical trials are listed once they are reviewed, approved, and ready for volunteer recruitment.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

An open source library built to reduce technical friction and help modelers share their work. Models within SSM can be used for inference of time-series analysis.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

A machine usable dictionary containing thousands of words, each with linguistic and psycholinguistic attributes (psychological measures are recorded for a small percentage of words). The dictionary may be of use to researchers in psychology or linguistics to develop sets of experimental stimuli, or those in artificial intelligence and computer science who require psychological and linguistic descriptions of words.

• Resource
• NIF
• 10 years ago - submitted by Maryann Martone

Core facility that utilizes a ThermoFisher Cellomics ArrayScan VTI instruments and associated automated cellular analysis software. The High Content Screening (HCS) Core provides a multiplexed functional screening and imaging platform to perform multi-well cell-based assays.

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• SciCrunch
• 10 years ago - by Anonymous

A GDS and OASIS file viewer editor that has file overlay and file creation capabilities. It features include: layer grouping, flexible rulers, image overlay, partial editing functions, and external library support.

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• RRID-Legacy
• 10 years ago - by Anonymous

Interactive application for data analysis and visualization in the form of plots. Its main feature is its usability and its simple graphical user interface. SciDAVis runs on GNU/Linux, Windows and MacOS X.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Web based resource focused on the genetics and genomics of immunologically related human diseases. Their mission is to provide a curated and integrated set of datasets and tools to support and promote research in this area. The current focus of the site is to integrate and curate summary case/control association statistics from the consortium of 12 diseases originally targeted by the ImmunoChip consortium.

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• SciCrunch
• 10 years ago - submitted by Ko-Wei Lin

A collaborative research project that supports nPOD approved diabetes investigators by freely providing rare and difficult-to-obtain tissues from type 1 and type 2 diabetes donors. Interested researchers are encouraged to apply to obtain nPOD tissues, or to request access to analyze cases in the nPOD Online Pathology site. Interested donors can contact nPOD directly for more information.

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• dkNET
• 10 years ago - submitted by Ko-Wei Lin