Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator.

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• SciCrunch
• 12 years ago - by Anonymous

A nonprofit health organization that works to improve the quality of life of Canadians affected by Alzheimer's disease and other dementias. This organization also supports research on the cause and potential cures for the disease through education and funding.

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• SciCrunch
• 12 years ago - by Anonymous

Sampling protocols produced by the BrainNet Europe Consortium generally with five types of dissection and brain processing procedures defined in all disease related protocols. * Fresh brain dissection * Fresh brain processing * Dissection of formalin-fixed brain * Histology and immunohistochemistry * Processing fresh brain

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• SciCrunch
• 12 years ago - by Anonymous

A biotech company that commercializes its patented Red/ET recombination worldwide as licenses and supplies several products for the pharmaceutical and biotech industry as well as academia. It operates from the Technologie Park in Heidelberg and provides customized in-house DNA modification of any kind. Recombineering with Red/ET allows cloning, subcloning and modification of DNA at any chosen position. It permits precise engineering of DNA molecules of any size, including very large ones such as BACs or the E.coli chromosome.

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• SciCrunch
• 12 years ago - by Anonymous

MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.

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• SciCrunch
• 12 years ago - by Anonymous

Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.

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• SciCrunch
• 12 years ago - by Anonymous

Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70).

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• SciCrunch
• 12 years ago - by Anonymous

Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.

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• SciCrunch
• 12 years ago - by Anonymous

A searchable and browsable index of neuroscience resources available on the internet including neurobiology, neurology, neurosurgery, psychiatry, psychology, cognitive science sites and information on human neurological diseases. Two categories exist: Best Bets and Cutaneous Fields of Peripheral Nerves.

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• SciCrunch
• 16 years ago - by Anonymous

An ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.

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• SciCrunch
• 12 years ago - by Anonymous

Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

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• SciCrunch
• 12 years ago - by Anonymous

Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.

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• SciCrunch
• 12 years ago - by Anonymous

The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 12 years ago - by Anonymous

A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It contains information about segmental duplications in the genomes of chimpanzee, mouse, and rat. The criteria used to identify regions of segmental duplication are: * Sequence identity of at least 90% * Sequence length of at least 5 kb * Not be entirely composed of repetitive elements. BACKGROUND: The high quality of the mouse genome draft sequence and its associated annotations are an invaluable biological resource. Identifying recent duplications in the mouse genome, especially in regions containing genes, may highlight important events in recent murine evolution. In addition, detecting recent sequence duplications can reveal potentially problematic regions of the genome assembly. We use BLAST-based computational heuristics to identify large (>/= 5 kb) and recent (>/= 90% sequence identity) segmental duplications in the mouse genome sequence. Here we present a database of recently duplicated regions of the mouse genome found in the mouse genome sequencing consortium (MGSC) February 2002 and February 2003 assemblies. RESULTS: We determined that 33.6 Mb of 2,695 Mb (1.2%) of sequence from the February 2003 mouse genome sequence assembly is involved in recent segmental duplications, which is less than that observed in the human genome (around 3.5-5%). From this dataset, 8.9 Mb (26%) of the duplication content consisted of "unmapped" chromosome sequence. Moreover, we suspect that an additional 18.5 Mb of sequence is involved in duplication artifacts arising from sequence misassignment errors in this genome assembly. By searching for genes that are located within these regions, we identified 675 genes that mapped to duplicated regions of the mouse genome. Sixteen of these genes appear to have been duplicated independently in the human genome. From our dataset we further characterized a 42 kb recent segmental duplication of Mater, a maternal-effect gene essential for embryogenesis in mice. CONCLUSION: Our results provide an initial analysis of the recently duplicated sequence and gene content of the mouse genome. Many of these duplicated loci, as well as regions identified to be involved in potential sequence misassignment errors, will require further mapping and sequencing to achieve accuracy. A Genome Browser database was set up to display the identified duplication content presented in this work. This data will also be relevant to the growing number of investigators who use the draft genome sequence for experimental design and analysis. The segmental duplication data and summary statistics are available for download and can also be visualized in a genome browser in the GBrowse section. Selected annotation tracks (except the segmental duplication track) have also been obtained from UCSC and loaded into the genome browser. Detailed information (e.g. overlapping genes, overlapping clones, detailed alignment) can be obtained by clicking on a duplication cluster in GBrowse. Both keyword search and BLAT search are available. Analyses based on previous genome assemblies can be found in the Previous Analyses section. Recent Developments The Non-Human Genome Segmental Duplication Database is continually updated including the archived copies of the analysis of all previous genome assemblies and will include all new species as they become available. Acknowledgments We thank The Centre for Applied Genomics at the Hospital for Sick Children (HSC) as well as collaborators worldwide. Supported by Genome Canada the Howard Hughes Medical Institute International Scholar Program (to S.W.S.) and the HSC Foundation.

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• SciCrunch
• 16 years ago - by Anonymous

Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).

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• SciCrunch
• 12 years ago - by Anonymous

Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

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• SciCrunch
• 12 years ago - by Anonymous

An open mark-up language for NMR data.

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• SciCrunch
• 12 years ago - by Anonymous