Curator Dashboard

A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Database of biological collections in natural history museums, herbaria, and other biorepositories resulting from a merger of Index Herbariorum (IH), Biodiversity Collections Index (BCI) and biorepositories.org. It contains more than 14,000 records for biorepository institutions, their collections, and staff members. Their two main goals are to improve access to information about biorepositories, the collections and specimens they house, and the researchers and collection managers who work there; and to facilitate electronic linkages to this information through web services that will rely on unique identifiers assigned to biorepositories and collections. The Consortium for the Barcode of Life (CBOL) has developed and will manage GRBio in collaboration with IH and BCI and in consultation with GBIF and NCBI. GRBio includes four categories of data records that provide information on: * Institutional repositories such as museums, herbaria, botanical gardens, zoos, biomedical research institutes and culture centers; * Institutional collection records such as the bird, algal or insect collections within an institutional repository; * Personal collections such as field samples held by a researcher before they have been accessioned into an institutional collection, or privately owned specimens held by non-researchers; and * Staff members at institutional repositories GRBio operates as a moderated community-curated resource. The community is invited to check and update their records and to register institutions, collections and staff members that have not already been registered. GRBio offers registration of institutional collections, "personal" research collections that have not yet been accessioned into an institutional repository, and privately owned collections.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

STRFPak is a Matlab toolbox for estimating the linear and nonlinear stimulus-response mapping function of sensory systems. This mapping function is commonly called the spatio- or spectro-temporal receptive field (STRF). A quantitative estimate of the STRF can be used in subsequent computational modeling studies or to predict future responses of the system. STRFPak implements several general STRF estimation techniques and can be used with any stimuli (including natural scenes and sounds). The theoretical basis for STRF estimation has been known for some time, but estimation software has not been widely available. This project aims to develop appropriate software and make it available to the wider community of sensory neuroscientists. Although STRFPak is based on established methods it incorporates two important innovations. First, STRFPak can be used to characterize a sensory system from its response to arbitrary stimuli including natural signals (e.g., vocalizations, natural scenes). Second, STRFPak incorporates several methods for estimating nonlinear STRFs. STRFPak also includes tutorial examples and documentation.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A community-defined, uniform, generic description of the core attributes of biological databases. The BioDBCore checklist is overseen by the International Society for Biocuration (ISB), in collaboration with the BioSharing forum. A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them have been partly compiled with the support of Oxford University Press and Re3Data.org. Database providers are encouraged to either create or claim their BioDBCore entry and update it as appropriate., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software application - part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Software R package for RNA-Seq Differential Expression Analysis.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Sage Bionetworks video podcasts feature the plenary talks from the April 2011 Commons Congress in San Francisco. The Keynote and project update video posts are in reverse chronological order; the full agenda is available at www.sagecongress.org. There are also several excellent podcasts from the January 2011 Symposium on Human Data Interoperability. The podcasts are also available on iTunes where you can subscribe and receive new podcasts automatically when posted. Upcoming posts will feature presentations and interviews on network biology, genomics, healthcare and open science. All these podcasts feature research and thought leaders as well as policy advocates, scientists working at the coal-face and patients. The topics span technical and strategic issues and include fact and opinion. The goal is to engage, educate and inspire non-scientists and scientists alike.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.

• Organization
• Consortia-pedia, a FasterCures Project
• 12 years ago - submitted by Taylor Cronin

Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Non-profit biomedical research organization developing predictors of disease and accelerating health research through creation of open systems, incentives, and standards. Formed to coordinate and link academic and commercial biomedical researchers through Commons that represents new paradigm for genomics intellectual property, researcher cooperation, and contributor evolved resources.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

The Osteoarthritis Biomarkers Project (OABP) is a consortium designed to identify and classify biological markers of progression of knee osteoarthritis. Their goal is to advance the ability to predict the individual risk of developing severe OA and to monitor progression of OA.

• Organization
• Consortia-pedia, a FasterCures Project
• 12 years ago - submitted by Taylor Cronin

Software tool for base and quality calling of trace files from DNA sequencing instruments.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Key Driver Analysis (KDA) is an analysis tool, as both an R package and Cytoscape plugin, for identifying key regulators of a gene regulatory network. It takes as input a gene network N (directed or undirected) and a gene set (module) G. The gene set is any subset of genes from the network N (e.g. pathway, module, ontology), permitting focus on a particular biological context. The KDA archive contains the plugin source, the plugin jar file, and several example datasets. Prerequisites: *Java, 5.0+ (www.javasoft.com) *Cytoscape, 2.6+ (www.cytoscape.org)

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software tool for reformatting abstracts from original submission formats into a text encoding format for publishing on-line and book abstracts.

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

Software R package for download, setup and access of Intensive Care Unit data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented.

• Resource
• SciCrunch
• 3 years ago - submitted by Nicolas Bennett

A virtual database currently indexing the following scientific Job resources: Naturejobs, Monster, Indeed, Hays, jobs.ac.uk, New Scientist Jobs, Science Careers, Access-ScienceJobs.co.uk, TheScienceJobs.com, ScienceBlogs: Jobs, and It Takes 30.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

A database which holds summaries of landmark clinical trials. The topics of contributed articles range across various biomedical fields and disciplines such as immunology, nephrology, and urology.

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

Collaborative MRI facility that is jointly operated by the University of Pittsburgh and Carnegie Mellon University. Research neuroimaging facility, with focus on advanced data analytics and basic science research. Designed to support basic science research and next generation of brain scientists.

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

THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu.

• Resource
• SciCrunch
• 15 years ago - by Anonymous