Curator Dashboard

A software program for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR. In addition, it provides a virtual electrophotogram to help users choose the best PSC. It is a valuable tool for designing specific, no dimer formation and amplicons size constrained PSCs to improve the multiplex PCR experiments.

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• SciCrunch
• 12 years ago - by Anonymous

Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio.

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• SciCrunch
• 17 years ago - by Anonymous

Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

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• SciCrunch
• 12 years ago - by Anonymous

A web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term gene fishing refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA.

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• SciCrunch
• 13 years ago - by Anonymous

Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

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• SciCrunch
• 12 years ago - by Anonymous

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

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• SciCrunch
• 17 years ago - by Anonymous

Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required.

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• SciCrunch
• 12 years ago - by Anonymous

Ontology to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD), a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.

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• SciCrunch
• 13 years ago - by Anonymous

R package providing functions to assess and to compare the performance of risk prediction (survival) models.

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• SciCrunch
• 13 years ago - by Anonymous

Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

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• SciCrunch
• 12 years ago - by Anonymous

Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior.

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• SciCrunch
• 13 years ago - by Anonymous

An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. BODB offers a way to document computational models of brain function by linking each model to Brain Operating Principles (BOPs), related brain regions, Summaries of Simulation Results (SSRs)and Summaries of Experimental Data (SEDs) used either to design or to test the model. Tools are provided to search for related models and to compare their coverage of SEDs. This allows automatic benchmarking of a model against a cluster of models addressing similar BOPs or SEDs or brain regions. Tools allow display of brain imaging results against a human brain applet; a new tool will link data to a macaque brain applet.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Analytical tools. Archive files may be written in any format and may include explanatory figures, program sources, readme files, and other related files. The readme file describes the purpose and usage of the archive file. This data sharing framework allows users to improve the reproducibility of simulations. Users can browse the platform contents via branch sites (A catalogue of illusions, Visitope), which introduce user friendly view of items such as basic images and original artworks of visual illusions with high resolution. The items in Visiome Platform are useful not only for reproducing the published results, but also for advancing and expanding the research in Vision Science.

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• SciCrunch
• 17 years ago - by Anonymous

Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data.

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• SciCrunch
• 17 years ago - by Anonymous

Tool that computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol. The Dali method optimizes a weighted sum of similarities of intramolecular distances. Suboptimal alignments do not overlap the optimal alignment or each other. Suboptimal alignments detected by the program are reported if the Z-score is above 2; they may be of interest if there are internal repeats in either structure. SOAP Web services are also available.

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• SciCrunch
• 17 years ago - by Anonymous

Software that compares the nucleosome profiles generated by high-throughput sequencing between different conditions. It provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise.

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• SciCrunch
• 13 years ago - by Anonymous

Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

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• SciCrunch
• 16 years ago - by Anonymous

A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.

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• SciCrunch
• 12 years ago - by Anonymous