Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Data management software implemented in Java that facilitates the entry of data into a relational database. It guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses. Canned reports provide information on RNA samples, studies, slide maps and other pertinent data and a general SQL query window allows freeform access to the underlying database. MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials.

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• SciCrunch
• 13 years ago - by Anonymous

A dataset of brain region connectivity statements mined from neuroscientific literature. Users can search for brain regions and explore region connectivity.

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• SciCrunch
• 11 years ago - submitted by Tom Gillespie

Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

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• SciCrunch
• 13 years ago - by Anonymous

The goal of this follow-up study of mothers who participated in the Hyperglycemia and Adverse Pregnancy Outcomes (HAPO) study is to determine the levels of blood sugar during pregnancy that are linked to increased body fat in the child, as well as to determine the chances of a mother developing diabetes 8-12 years after the pregnancy. The original study examined 23,316 mother-child pairs, and researchers determined that the hyperglycemia of a mother was linked to newborn birth weight and body fat. HAPO-FUS will enroll 7,000 or the original HAPO mother-child pairs for one follow-up visit to assess body composition, blucose metabolism, medical history, and other metabolic parameters.

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

Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

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• SciCrunch
• 13 years ago - by Anonymous

A software dedicated to microbial ecology and environmental studies which uses individual nucleic sequences or consensus sequences produced by multiple alignments to design degenerate probes in order to target gene families covering many sequence variants. Probe specificity is assessed by similarity search against an exhaustive formatted database dedicated to microbial ecology containing coding sequences (CDS) and their putative 5-prime and 3-prime unstranslated regions (UTR). Potential cross-hybridizations identified by the program are clustered and results are organized in order to simplify user interpretation.

• RRID-Legacy
• 11 years ago - by Anonymous

Software C library for entropy measurement of byte streams and other data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

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• SciCrunch
• 13 years ago - by Anonymous

A research facility and clinical program that is dedicated to the study and the treatment of both normal aging and Alzheimer's disease. This facility will accommodate requests for its resources (for example, data or tissue) from investigators that are not funded by the ADRC. Their team is composed of experts in geriatrics, geriatric psychiatry and psychology, neurology, pathology, and radiology. All team members work to provide services to those with memory disorders. This center sponsors educational programs for healthcare professionals and community groups. Data from the ADRC cores are available to all ADRC investigators after approval from the PI who collected the data. Data generated by the ADRC cores are communicated to the National Alzheimer's Coordinating Center (NACC) and can be available through them. Tissue can be distributed after approval of the Tissue Allocation Committee, and can be used for further research.

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• SciCrunch
• 15 years ago - by Anonymous

Software C++11 library for next-gen sequence quality control and assessment.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Wiki of chemical and preparatory experimental protocols.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Doumented on September 23,2022. The National Cancer Institute initially established the Cooperative Prostate Cancer Tissue Resource (CPCTR) to provide prostate cancer tissue samples with clinical annotation to researchers. The Resource provides access to formalin-fixed, paraffin-embedded primary prostate cancer tissue with associated clinical and follow-up data for research studies, particularly studies focused on translating basic research findings into clinical application. Fresh-frozen tissue is also available with limited clinical follow up information since these are more recent cases. The Resource database contains pathologic and clinical information linked to a large collection of prostate tissue specimens that is available for research. Researchers can determine whether the Resource has the tissues and patient data they need for their individual research studies. Consultation and interpretive services: Assistance is available from trained CPCTR pathologists. The CPCTR can provide consultative assistance in staining interpretation, and scoring, on a collaborative basis. Fresh Frozen and Paraffin Tissue: The resource has over 7,000 annotated cases (including 7,635 specimens and 38,399 annotated blocks). Tissue Microarrays (TMA): The CPCTR has slides from prostate cancer TMAs with associated clinical data. The information provided for each case on the arrays (derived from radical prostatectomy specimens) includes: age at diagnosis, race, PSA at diagnosis, tumor size, TNM stage, Gleason score and grade, and vital status and other variables.

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• SciCrunch
• 16 years ago - by Anonymous

Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software that graphically displays correlation in microarray data that is due to insufficient normalization.

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• SciCrunch
• 13 years ago - by Anonymous

Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Mark up language for collecting and exchanging metadata in an automated, computer-based fashion, developed for neuroscience, specifically, neurophysiology experiments. In odML arbitrary metadata information is stored as extended key-value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability.

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• SciCrunch
• 14 years ago - by Anonymous

Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen