Curator Dashboard

Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A google drive interface for scientific big data. CyVerse cyberinfrastructure is applicable to all life sciences disciplines and works equally well on data from plants, animals, or microbes. It provides life scientists with computational infrastructure to handle large datasets and complex analyses. Its extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, and APIs.

• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Software tool for the design of multiplex pyrosequencing assays.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Consortium serving the diabetic complications community that sponsors annual meetings in complications-relevant scientific areas, solicits and funds pilot projects in high impact areas of complications research, and provides resources and data including animal models, protocols and methods, validation criteria, reagents and resources, histology, publications and bioinformatics for researchers conducting diabetic complications research.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

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.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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

• Resource
• 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.

• Resource
• 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.

• Resource
• 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.

• Resource
• 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.

• Resource
• 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.

• Resource
• 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.

• Resource
• 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.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

• Resource
• SciCrunch
• 14 years ago - by Anonymous

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

• Resource
• 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.

• Resource
• SciCrunch
• 14 years ago - by Anonymous