Curator Dashboard

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software wrapper to speed up downloading process by dividing the work into multiple threads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Questionnaire developed by physicians in NIDDK's Chronic Prostatitis Collaborative Research Network that can help physicians to accurately measure the severity of prostatitis symptoms and their impact on a patient's lifestyle. The CPSI questionnaire assesses pain, urination, and the effect of chronic prostatitis on daily activities. With this information, researchers and physicians can reliably evaluate whether potential treatments are working. The questionnaire was originally published in the Journal of Urology in August 1999 (Vol. 162, pages 369-375). It is available as a PDF document in English, Spanish, German and Korean.

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• dkNET
• 14 years ago - by Anonymous

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 10 years ago - by Anonymous

Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Network of clinical centers and a coordinating center that investigate the potential use of glucose monitoring technology and its impact on the management of type 1 diabetes in children. Specific goals for the network include the following: * Assess the accuracy of continuous monitoring devices in order to determine if these devices are useful in improving glycemic control and preventing hypoglycemia in children with T1DM. * Determine the optimal utilization of continuous glucose monitors in the management of T1DM in children. * Assess the impact of continuous glucose monitoring on quality of life for the child and family. * Develop tools for the child and parents to use for incorporating continuous glucose monitors into diabetes self-management. * To assess possible changes in neurocognitive function and how it relates to frequency of hypoglycemia in young children with type 1 diabetes. * Evaluate and develop distinct, age-appropriate treatment approaches to T1DM in children. * Use continuous glucose monitoring to characterize the glycemic profile of nondiabetic children. * Develop statistical methods for the analysis of continuous glucose monitoring data. Closed and active studies are listed along with the associated protocols, public datasets, and publications.

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• dkNET
• 14 years ago - by Anonymous

International effort whose objective is to improve and encourage the exchange of Metabolomics data. Datasets are stored in external data repositories independent of MetabolomeXchange; however, MetabolomeXchange allows users to browse datasets directly then proceed to the external repository for more information.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519.

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• SciCrunch
• 17 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Allows annotation of gene expression at all stages of development and tissue types (including sub cellular location) using standard Drosophila anatomy ontology. All methods of input use a controlled vocabulary to ensure data integrity.

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• SciCrunch
• 14 years ago - by Anonymous

P{sqh.EGFP.AA}

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• SciCrunch
• 10 years ago - submitted by Claudia Vasquez

Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.

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• SciCrunch
• 17 years ago - by Anonymous

Database of bacteriophage gene regulation elements, genes, and genomes. Data are collected from scientific papers and cross-referenced with other database resources. The database can be searched using keywords or browsed by phage genome. Sets of regulatory sequences can browsed and exported in various formats.

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• RRID-Legacy
• 10 years ago - submitted by Ivan Erill

Software R package provides some basic functions for filtering genes.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections.

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• SciCrunch
• 17 years ago - by Anonymous

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome

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• SciCrunch
• 17 years ago - by Anonymous

Software library of core preprocessing routines.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth