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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

Software tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. It can be used in prioritize functional SNPs in a genetic study. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 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

The purpose of this document is to give the exact definitions of the MORGAM cohorts and to describe their basic characteristics and data collection procedures, such as the follow-up procedures, the disease end-points recorded and diagnostic procedures. The definition and selection criteria for MORGAM cohort are described in section Definition and selection of cohorts of the MORGAM Manual. For convention, each cohort is assigned appropriate name and code number which is given in Table 1. The baseline characteristics of the MORGAM Cohorts are summarized in Table 2. An overall summary of MORGAM Cohorts along with the objectives of the Project has been published elsewhere [1]. Sponsor. The research was supported by the GenomEUtwin Project grant from the European Commission under the programme `Quality of Life and Management of the Living Resources'' of 5th Framework Programme (no. QLG2-CT-2002-01254) and by the Academy of Finland via its grant number 53646.

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• SciCrunch
• 17 years ago - by Anonymous

Software that determines genotypes for microsatellite repeats in high-throughput sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC).

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• SciCrunch
• 13 years ago - by Anonymous

Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera).

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• SciCrunch
• 15 years ago - by Anonymous

Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

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• SciCrunch
• 13 years ago - by Anonymous

A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025.Relational database of all significant published qualitative and quantitative information on cell signaling proteins. The Molecule Pages database was developed with the specific aim of allowing interactions, and indeed whole pathways, to be modeled. The goal is to filter the data to present only validated information. In addition, the Gateway is the home of Signaling Update, which provides a one-stop overview of the latest and hottest research in cell signaling for both the specialist and non-specialist alike.

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• SciCrunch
• 17 years ago - by Anonymous

Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

EMS is a freely available suite of Matlab functions and subroutines (with some externally compiled C routines) for fully-automated multi-spectral classification of brain tissues in Magnetic Resonance (MR) images. It uses a model based approach (including an explicit model for MR bias fields) in which all the model parameters are automatically estimated for each individual scan. This enables it to process large amounts of data from normal subjects and subjects suffering from Multiple Sclerosis without need for user intervention or preceeding manual training phase.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included.

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• SciCrunch
• 13 years ago - by Anonymous