Curator Dashboard

An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A database of plant protein kinases and phosphatases as well as genomic information for these enzymes. Because protein kinases and phosphatases control so many processes in plants, and occur in networks that unite different cellular processes, a genome wide approach is needed to make significant advances in discovering the roles of these enzymes in the regulation of plant function.

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• SciCrunch
• 17 years ago - by Anonymous

R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.

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• SciCrunch
• 13 years ago - by Anonymous

Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Génoplante rice insertion line library. To display the sequence information (Flanking Sequence Tags) resulting from the molecular characterization of the mutagen insertion sites in the collection, Oryza Tag Line is linked to OryGenesDB a GGB-derived interface or FLAGDB++ a Java based interface. Aside from generic data ( production record and seed stock ) Oryza Tag Line includes textual and pictorial information resulting from the following observations: (i.) GUS/GFP expression assays conducted on the primary transformants (T0) and/or T1 progenies (ii.) morpho-physiological alterations detected during the growth of the T1 progenies either in phytotron -up to the 5-6 leaf stage- or under agronomical conditions in the field (collaboration with CIAT, Cali, Colombia).

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• SciCrunch
• 17 years ago - by Anonymous

A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.

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• SciCrunch
• 13 years ago - by Anonymous

Located in Baltimore, MD., Kennedy Krieger Institute is an internationally recognized institution dedicated to improving the lives of children and adolescents with pediatric developmental disabilities and disorders of the brain, spinal cord and musculoskeletal system, through patient care, special education, research, and professional training. Patient Care--Specialists from various fields and disciplines work together to evaluate, diagnose, and create individualized treatment plans to guide patients and families through all stages of care. Research and Professional Training--Our innovative research and professional training programs are leading the way in the understanding, prevention, and treatment of a wide range of developmental disabilities. Special Education--We offer a number of school-based, hospital-based, and recreational programs designed to unlock the promise inside our students through innovative and customized educational approaches. Community--We are committed to helping people with developmental disabilities achieve their potential and enjoy success in community life by providing access to resources, services, and model programs.

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• SciCrunch
• 15 years ago - submitted by Stephen Larson

An antibody information database where antibodies are organized by the target protein UniProt id.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.<BR/> Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course.<BR/> User Requirements: Please read for important information on scripting NCBI servers.<BR/> EInfo: Provides field index term counts, last update, and available links for each database.<BR/> ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment.<BR/> EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies.<BR/> ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment.<BR/> EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment.<BR/> ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs.<BR/> EGQuery: Provides Entrez database counts in XML for a single search using Global Query.<BR/> ESpell: Retrieves spelling suggestions.<BR/> SOAP Interface for Entrez Utilities<BR/> PMID to PMC ID Converter<BR/> Entrez DTDs<BR/> Demonstration Program<BR/> Announcement Mailing List<BR/> Leasing Data from the National Library of Medicine<BR/> Help Desk<BR/> User Requirements<BR/> Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following:<BR/> Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests.<BR/> Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address.<BR/> Make no more than 3 requests every 1 second.<BR/> Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem.<BR/> NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.<BR/>

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• SciCrunch
• 17 years ago - by Anonymous

An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa

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• SciCrunch
• 13 years ago - by Anonymous

Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.

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• SciCrunch
• 13 years ago - by Anonymous

The EIB provides assessment tests for substance disorder related clinical instruments that are freely available. Details regarding copyright and/or possible use restrictions are specified for each instrument. Instruments are generally classed according to the intervention field they are designed to be used in (treatment, prevention, or harm reduction), though some instruments may be usable in more than one field.

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• SciCrunch
• 17 years ago - by Anonymous

A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies.

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• SciCrunch
• 13 years ago - by Anonymous

A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images.

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• SciCrunch
• 13 years ago - by Anonymous

Software for detecting transcription factor binding sites from ChIP-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Software tools for the analysis of enrichment-based epigenomic data.

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• SciCrunch
• 13 years ago - by Anonymous

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

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• SciCrunch
• 13 years ago - by Anonymous

QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. QccPack is intended for use in the development of prototypes of coding and compression systems, and in academic research. QccPack includes routines for entropy coding, scalar quantization, vector quantization, and wavelet transforms. Additonally, an open-source implementation of SPIHT is available as an optional module. QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. The essential component of the QccPack collection is a library (a static library, libQccPack.a, and, if supported on your system, a dynamic library, libQccPack.so) of procedures implementing a large variety of compression and coding algorithms. Application programs may make use of the QccPack library routines by linking the application against the library during compilation. Each library function is very general in its implementation so to be useful in a large variety of applications. Additionally, much of the functionality of the library routines has been provided in the form of stand-alone executable programs. Probably the prime importance of these utility programs is that they provide examples of how to interface with many of the QccPack library routines. The utility programs could also be called from scripts to simulate the operation of complex coding and compression systems before implementing all the system functionality into one stand-alone program. Currently, QccPack consists of over 55,000 lines of C code implementing over 500 library routines and over 50 stand-alone utility programs. The major functionalities currently implemented include: * Entropy coding o Arithmetic coding including multiple-context adaptive and nonadaptive models o Huffman coding o Golomb and adaptive Golomb coding * Scalar Quantization (SQ) o Uniform SQ o Dead-zone SQ o -law and A-law SQ o Lloyd algorithm for optimal SQ design * Vector quantization (VQ) o Generalized Lloyd algorithm (GLA) for VQ-codebook design o Full-search VQ encoding and decoding o Entropy-constrained-VQ (ECVQ) training, encoding, and decoding o Multistage VQ (MSVQ) (also called residual VQ (RVQ)) training, encoding, and decoding * Adaptive vector quantization (AVQ) o The generalized-threshold-replenishment (GTR) algorithm o The Paul algorithm o Gersho-Yano algorithm o Coding of side information * Wavelet transforms, wavelet-based subband coding o Discrete wavelet transform (DWT) using first-generation filter banks and popular orthonormal and biorthogonal wavelets o Lifting implementations of DWT for popular wavelets o Two-dimensional DWT in the form of dyadic subband pyramids o Three-dimensional DWT in the form of dyadic subband pyramids as well as a packet transform o Shape-adaptive DWT (SA-DWT) for 1D and 2D signals o Redundant DWT (RDWT), aka, the algorithme trous o The SR algorithm for wavelet-based image coding o The SFQ algorithm for wavelet-based image coding o The WDR algorithm for wavelet-based image coding o The 3D-WDR algorithm for wavelet-based image-cube coding o The tarp-filter algorithm for wavelet-based image coding o The 3D-tarp algorithm for wavelet-based image-cube coding o The TCE algorithm for wavelet-based image coding o The BISK algorithm for wavelet-based shape-adaptive image coding o The 3D-BISK algorithm for wavelet-based image-cube coding * Error-correcting codes o Field arithmetic, including Gaussian-elimination matrix inversion o Reed-Solomon encoding and decoding o CRC codes o Trellis codes o Hard and soft Viterbi decoding * Image processing o Routines for reading and writing gray and color still images and sequences of images (via PGM and PPM formats) o Routines for reading and writing 3D image-cube volumes o Image and image-sequence deinterlacing o Image differential-pulse-code modulation (DPCM) o Color-space conversions: RGB, YUV, CIE XYZ, CIE UCS, CIE modified UCS o Block-based DCT and inverse DCT * Video coding o The spatial-block algorithm for image-sequence coding o The RDWT-block algorithm for image-sequence coding o The RWMH algorithm for image-sequence coding o Block-based motion estimation and motion compensation o Motion estimation and motion compensation using regular triangle meshes o Encoding and decoding of motion-vector fields * General routines o Vector math (up/down sampling, sorting, dot product, addition/subtraction, etc.) o Matrix math (addition/subtraction, vector-matrix multiplication, etc.) o Linked lists and associated operations o Entropy estimation (first and second order) o General file input and output, including automatic detection and reading/writing of gzip-compressed files o Character bit-packing for binary bitstream input/output o Memory-based fifo for binary bitstreams o Conversion between various file formats used by library routines o Error-message tracking, formatting, and output o Automatic command-line parameter parsing In addition to the standard functionalities listed above, there exist optional modules that can be added to the QccPack library. Usually, these modules are available under licensing terms different from the GPL/LGPL licenses of QccPack and may contain patented algorithms; refer to the documentation included with each module for specific details. These modules are downloaded separately from QccPack and are not enabled by default during the building of QccPack. The currently available optional modules and their functionalities are: * QccPackSPIHT o The Set Partitioning in Hierarchical Trees (SPIHT) algorithm for wavelet-based image coding * QccPackSPECK o The Set-Partitioning Embedded Block (SPECK) algorithm for wavelet-based image coding Abstract: We describe the QccPack software package, an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack is being written to expedite data-compression research and development by providing general and reliable implementations of common compression techniques. Functionality of the current release includes entropy coding, scalar quantization, vector quantization, adaptive vector quantization, wavelet transforms and subband coding, error-correcting codes, image-processing support, and general vector-math, matrix-math, file-I/O, and error-message routines. All QccPack functionality is accessible via library calls; additionally, many utility programs provide command-line access. The QccPack software package, downloadable free of charge from the QccPack Web page, is published under the terms of the GNU General Public License and the GNU Library General Public License which guarantee source-code access and as well as allow redistribution and modification. Additionally, there exist optional modules that implement certain patented algorithms. These modules are downloadable separately and are typically issued under licenses that permit only non-commercial use. This material is based upon work supported in part by the National Science Foundation under Grant No. INT-9600260.

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• SciCrunch
• 17 years ago - by Anonymous

ZFIN Protocol Wiki is where zebrafish researchers can share experimental protocols and tips with the rest of the research community. Protocols are organized into sections corresponding to the chapters of The Zebrafish Book, 5th edition (4th edition on-line). Feel free to add new protocols to the appropriate section or add comments to any existing protocol. Sections * General Methods for Zebrafish Care * Breeding * Embryonic and Larval Culture * Imaging * Cellular Methods * Dissociated Cell Culture * Genetic Methods * Antisense Methods * Histological Methods * in situ Hybridization Techniques * Mapping * Transgenesis * Gene Cloning * DNA Analysis * RNA Analysis * Protein Analysis * Microarray * Recipes

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• SciCrunch
• 16 years ago - by Anonymous

MIMIC II (Multiparameter Intelligent Monitoring in Intensive Care) Database contains comprehensive clinical data from tens of thousands of Intensive Care Unit (ICU) patients. Data were collected between 2001 and 2008 from a variety of ICUs (medical, surgical, coronary care, and neonatal) in a single tertiary teaching hospital. The database contains clinical data from bedside workstations as well as hospital archives. The database also includes thousands of records of continuous high-resolution physiologic waveforms and minute-by-minute numeric time series (trends) of physiologic measurements.

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• SciCrunch
• 16 years ago - by Anonymous