Curator Dashboard

Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. A command line program in Unix to convert images to a variety of formats (PNG, TIFF, JPEG, PPM..etc). It is uniquely different from other programs such as Adobe Photoshop or ImageMagick because it is designed for dealing with the high-resolution images with file sizes of several gigabytes. Image Converter does not require any additional RAM or virtual memory to run. Also, run-time is relatively fast for high resolution data.

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• SciCrunch
• 13 years ago - by Anonymous

30 sections from a serial section Transmission Electron Microscopy (ssTEM) data set of the Drosophila first instar larva ventral nerve cord (VNC). The microcube measures 2 x 2 x 1.5 microns approx., with a resolution of 4x4x50 nm/pixel. The images are representative of actual images in the real-world: there is a bit of noise; there are image registration errors; there is even a small stitching error in one section. None of these led to any difficulties in the manual labeling of each element in the image stack by an expert human neuroanatomist. A software application that aims at removing or reducing human operation must be able to cope with all these issues. Each labeled object has a unique id and fits into the overall datastructure of the data set. For example, each mitochondria is represented by a unique Arealist object, containing a list of labeled areas, one per section. All membranes have been highlighted as one unique object. All neurites (and glia) have been highlighted each as its own independent object, delimited by membrane and non-overlapping with membrane and with each other. On the other hand, mitochondria, noise and synapses overlap with membranes, neurites and glia; hence, they are offered as independent tif stacks.

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• SciCrunch
• 14 years ago - by Anonymous

This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction.

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• SciCrunch
• 16 years ago - by Anonymous

Database of the nation''s substance abuse and mental health research data providing public use data files, file documentation, and access to restricted-use data files to support a better understanding of this critical area of public health. The goal is to increase the use of the data to most accurately understand and assess substance abuse and mental health problems and the impact of related treatment systems. The data include the U.S. general and special populations, annual series, and designs that produce nationally representative estimates. Some of the data acquired and archived have never before been publicly distributed. Each collection includes survey instruments (when provided), a bibliography of related literature, and related Web site links. All data may be downloaded free of charge in SPSS, SAS, STATA, and ASCII formats and most studies are available for use with the online data analysis system. This system allows users to conduct analyses ranging from cross-tabulation to regression without downloading data or relying on other software. Another feature, Quick Tables, provides the ability to select variables from drop down menus to produce cross-tabulations and graphs that may be customized and cut and pasted into documents. Documentation files, such as codebooks and questionnaires, can be downloaded and viewed online.

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• SciCrunch
• 17 years ago - by Anonymous

A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470.

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• SciCrunch
• 13 years ago - by Anonymous

Collection of curated structural variation in the human genome. Catalogue of human genomic structural variation identified in healthy control samples for studies aiming to correlate genomic variation with phenotypic data. It is continuously updated with new data from peer reviewed research studies. The Database is no longer accepting direct submission of data as they are currently part of a collaboration with two new archival CNV databases at EBI and NCBI, called DGVa and dbVAR, respectively. One of the changes to DGV as part of this collaborative effort is that they will no longer be accepting direct submissions, but rather obtain the datasets from DGVa (short for DGV archive). This will ensure that the three databases are synchronized, and will allow for an official accessioning of variants.

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• SciCrunch
• 17 years ago - by Anonymous

The primary climate-change data and information analysis center of the U.S. Department of Energy (DOE) and includes the World Data Center for Atmospheric Trace Gases, serving the climate change-related data and information needs of users worldwide. CDIAC''s data holdings include estimates of carbon dioxide emissions from fossil-fuel consumption and land-use changes; records of atmospheric concentrations of carbon dioxide and other radiatively active trace gases; carbon cycle and terrestrial carbon management datasets and analyses; and global/regional climate data and time series. CDIAC provides scientific and data management support for projects sponsored by a number of agencies, including the AmeriFlux Network, continuous observations of ecosystem level exchanges of CO2, water, energy and momentum at different time scales for sites in the Americas; the Ocean CO2 Data Program of CO2 measurements taken aboard ocean research vessels; DOE-supported FACE experiments, which evaluate plant and ecosystem response to elevated CO2 concentrations; and the HIPPO project, which is analyzing the atmospheric carbon cycle and greenhouse gas concentrations from pole to pole over the Pacific Ocean. For those wishing to contribute data to the CDIAC data collection, review the guide and then contact one of the CDIAC staff members to discuss further data submission plans. Data providers may submit data in a variety of ways including via email, direct deposit to a secure CDIAC File Transfer Protocol (FTP) server, on transfer media (e.g. CD-ROM), or by having CDIAC mirror a location at the investigator''s institution.

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• SciCrunch
• 14 years ago - by Anonymous

Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A cooperative research program to explore the issues related to the complex system of offender treatment services. Nine research centers and a Coordinating Center were created in partnership with researchers, criminal justice professionals, and drug abuse treatment practitioners to form a national research infrastructure. The establishment of CJ-DATS is an outstanding example of cooperation among Federal agencies with the research community... We need to understand how to provide better drug treatment services for criminal justice offenders to alter their drug use and criminal behavior. - Dr. Nora Volkow, Director of NIDA. CJ-DATS PHASE I In 2002, NIDA launched the National Criminal Justice����������Drug Abuse Treatment Studies (CJ-DATS). CJ-DATS is a multisite research program aimed at improving the treatment of offenders with drug use disorders and integrating criminal justice and public health responses to drug involved offenders. From 2002 through 2008, CJ-DATS researchers from 9 research centers, a coordinating center, and NIDA worked together with federal, state, and local criminal justice partners to develop and test integrated approaches to the treatment of offenders with drug use disorders. The areas that were studied included: * Assessing Offender Problems * Measuring Progress in Treatment and Recovery * Linking Criminal Justice and Drug Abuse Treatment * Adolescent Interventions * HIV and Hepatitis Risk Reduction * Understanding Systems CJ-DATS PHASE II In 2008, CJ-DATS began to focus on the problems of implementing research-based practices drug treatment practices. This research concerns the organizational and systems processes involved in implementing valid, evidence-based practices to reduce drug use and drug-related recidivism for individuals in the criminal justice system. 12 CJ-DATS Research Centers are conducting implementation research in three primary domains: * Research to improve the implementation of evidence-based assessment processes for offenders with drug problems * Implementing effective treatment for drug-involved offenders * Implementing evidence-based interventions to improve an HIV continuum-of-care for offenders

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• SciCrunch
• 17 years ago - by Anonymous

A knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on: 1. primary sequence 2. known or predicted secondary structure 3. known or predicted tertiary contacts (optional) Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures. NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data. Imported from BiositeMaps registry

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• SciCrunch
• 14 years ago - by Anonymous

MEDLINE (Medical Literature Analysis and Retrieval System Online) is the U.S. National Library of Medicine''s (NLM) premier bibliographic database that contains over 16 million references to journal articles in life sciences with a concentration on biomedicine. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by NLM''s National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Currently, citations from approximately 5,200 worldwide journals in 37 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations. The subject scope of MEDLINE is biomedicine and health, broadly defined to encompass those areas of the life sciences, behavioral sciences, chemical sciences, and bioengineering needed by health professionals and others engaged in basic research and clinical care, public health, health policy development, or related educational activities. MEDLINE also covers life sciences vital to biomedical practitioners, researchers, and educators, including aspects of biology, environmental science, marine biology, plant and animal science as well as biophysics and chemistry. Sponsors: Services/products providing access to MEDLINE data are also developed and made available by organizations that lease the database from NLM.

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• SciCrunch
• 17 years ago - by Anonymous

Software to help researchers process scientific papers faster and get the information they are interested in out of them. This is achieved by automating the recognition of core scientific concepts such as Motivation, Method, Result, Conclusion in papers and uses them to generate automatic summaries. This SAPIENTA tool adds additional functionality to the SAPIENT tool, an annotation tool implemented as a web application which enables experts to annotate scientific papers, sentence by sentence manually, according to the Core Scientific Concept (CSC) schema.

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• SciCrunch
• 15 years ago - by Anonymous

Clinical study that investigated several hundred families with two or more blood relatives with interstitial cystitis in order to understand the molecular genetic basis of this condition. The study sought to find changes in genes that are found far more commonly in family members who have interstitial cystitis than in those who do not have the disease. Identifying these genes should lead to a better understanding of the cause of interstitial cystitis. This is a national study which is conducted by telephone and mail, and in which participants could participate entirely from their home.

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• dkNET
• 14 years ago - by Anonymous

Project to improve data and sample exchanges and to facilitate large scale analysis of data by improving interoperability of French Biological Resources Centres (BRC or biobanks) IT systems and biological databases. The work done in this project will be linked to other national (IBiSA, ANR, R��seau des Biobanques, Club 3C-R), European (BBMRI, ELIXIR) or international project (P3G). In the preliminary phase (2009-2010) I3-CRB has developed a directory of French Biological Resource Centres / Biobanks where one may register their French BRC or perform a search across all of them. Detail by overall data or kingdom is provided as well as many filtering options. Access to biological samples is provided by the participating BRC''''s. Biological Resources Centres (BRC or biobanks) collect annotated biological samples from various sources (human, animal, plant, bacteria...). The type of samples depends on the collection and the associated thematic (DNA, proteins, cells, tissues, blood, serum, organisms...). The aims of these centers are to collect, to store, to transform and to distribute the biological samples. They constitute a vital infrastructure for life science and health research. Goals of the French Biobanks/Biological Resource Centres: * List French biobanks and their biological collections * Improve sample exchanges * Improve the international visibility of the French biological collections MeSH terms have been integrated: Domains, diseases, and location of the disease (Anatomy). Collections/species are based on NCBI Taxonomy.

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• SciCrunch
• 15 years ago - by Anonymous

It was created to host functional genomic information gathered as part of a large NSF funded rice kinase proteomics project. The goal is to integrate disparate data sets into a logical, user friendly format. To accomplish this, they have developed a platform to display user selected functional genomic data on a phylogenetic tree. The RKD also includes an interactive chromosomal map showing the positions of all rice kinases and an interactive protein-protein interaction maps.

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• SciCrunch
• 17 years ago - by Anonymous

A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. It uses a visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom ''gene card'' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. A complete listing of the species and strains in the BacMap database is available on the BacMap homepage. Below each species/strain name is a list of the sequenced chromosomes and plasmids that are available. Some features of BacMap include: * Maps are available for 2023 bacterial chromosomes. * Each map supports zooming and rotation. * Map gene labels are hyperlinked to detailed textual annotations. * Maps can be explored manually, or with the help of BacMap''s built in text search and BLAST search. * A written synopsis of each bacterial species is provided. * Several charts illustrating the proteomic and genomic characteristics of each chromosome are available. * Flat file versions of the BacMap gene annotations, gene sequences and protein sequences can be downloaded. BacMap can be used to: * Obtain basic genome statistics. * Visualize the genomic context of genes. * Search for orthologues and paralogues in a genome of interest. * Search for conserved operon structure. * Look for gene content differences between bacterial species. * Obtain pre-calculated annotations for bacterial genes of interest.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 29,2019.<br/><br/>Locus-specific database listing variants of the SCN1A gene. To provide a continued platform that is in keeping with the latest data, this web site has been set up where all information can be accessed and downloaded. A Mutation submission form encourages data submissions. Over the past ten years, mutations in voltage-gated sodium channels (Navs) have become closely associated with inheritable forms of epilepsy. One isoform in particular, Nav1.1 (gene symbol SCN1A), appears to be a superculprit, with virtually hundreds of mutations. The associated phenotypes range from benign febrile seizures to extremely serious conditions like Dravet syndrome (a.k.a. severe myoclonic epilepsy in infancy or SMEI). Despite the wealth of information, mutational analyses are cumbersome, owing to inconsistencies among the Nav1.1 sequences to which different research groups refer. Splicing variability is the core problem: Nav1.1 exists in the brain in 3 different isoforms: full-length (2009 AA) as well as two shorter versions that lack 11 or 28 amino acids compared to the former. This online database ?????? SCN1A infobase ?????? establishes a standardized nomenclature for Nav1.1 variants so as to provide a platform from which future mutation analyses can be started without up-front data normalization.

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• SciCrunch
• 16 years ago - by Anonymous