MEDALS Tool catalog Others

ADMER2

[ Official site ] [ Show detail ]	Summary	"ADMER* ver.1.5.1e is a series of models and systems designed for estimating atmospheric levels of chemicals and assessing their exposure, developed by the National Institute of Advanced Industrial Science and Technology(AIST). The functions include:* Generation and confirmation of meteorological data* Generation and confirmation of chemical substance emission data* Calculation of atmospheric levels and depositions of chemicals* Graphical images of calculation results* Calculation result Histogram* Population exposure assessment*Official Name for AIST-ADMER :National Institute of Advanced Industrial Science and Technology - Atmospheric Dispersion Model for Exposure and Risk Assessment "
	Data type	Chemical compound AMEDAS data of intended year (used to create weather data) Discharge data of intended chemical substance (used to create grid discharge data)

BioDBScan

[ Official site ] [ Show detail ]	Summary	"BioDBScan is a free web-based application that alerts you when any data about genes, proteins, chemicals or drugs of your interest is newly released in world-renowned databases such as NCBI, Ensembl, DrugBank and others. It delivers an E-mail message every Monday if any data is detected by the Hyperlink Management System.BioDBScan was developed as a new function of PubMedScan by 2011-2012 METI Life-science Database Project. It is operated by Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology."
	Data type	"genes, pathways, diseases, etc."

CADLIVE

[ Official site ] [ Show detail ]	Summary	"CADLIVE is a system for constructing large-scale biological networks (metabolic andgene regulatory networks) using GUI (Graphic User Interface) and saving them asregulator reaction equations in a database in the format compatible to a simulator.The System consists of the CADLIVE GUI Network Constructor, the Pathway Search Program for Virtual Knockout Mutants, the CADLIVE Grid Layout Program, the CADLIVE Dynamic Simulator, and the CADLIVE Metabolic Engineering Tools. The Network Constructor enables one to construct large-scale biochemical network maps. The Pathway Search Program for Virtual Knockout Mutants explores all possible pathways between two species and can be applied to a knockout mutant. The Grid Layout Program automatically layouts biochemical networks on two-dimensional squared grid. The Dynamic Simulator automatically converts biochemical network maps into dynamic models and simulates their dynamics. The Metabolic Engineering Tools are developed as elementary mode based algorithms.Some part of the system development had been conducted by financial support from NEDO project. "
	Data type	Metabolite repression

CARCINOscreen

[ Official site ] [ Show detail ]	Summary	"CARCINOscreen is using a group of genes to measure the amount of gene expression in rat liver treated with compounds that are customized for the prediction of carcinogenicity, to predict the carcinogenic risk of compounds at an early stage. Carcinogenicity studies with rodents is usually required for two years as the administration period, in this system can be applied to biological samples obtained by short-term administration of 14 or 28 days is a great feature (Translated from the original site). This system has been commercialized as a service contract analysis."
	Data type	Chemical compound

Dr DMASS

[ Official site ] [ Show detail ]	Summary	"Software Dr DMASS which has been developed to effectively analyze mass spectral data using multivariate analysis consist of three steps, (i) Peak Correction, (ii) Multivariate Data Processing, and (iii) Multivariate Analysis. In Peak Correction process, we correct experimental m/z values based on the relation between experimental and desired values in internal mass calibrants (IMCs). This software and its instruction manual is freely available at the present site. Java j2sdk-1.4.2. is required to be installed in the user's computer to use this software. (cited from the original site)"
	Data type	mass spectral data

Dr DMASS+

[ Official site ] [ Show detail ]	Summary	"Software DrDMASS+ has been developed to effectively analyze mass spectral data based on multivariate analysis. A flow diagram of Data processing consists of four stages, (i) Peak Correction, (ii) Multivariate Data Processing, (iii) Unsupervised Learning, and (iv) Supervised Learning(cited from the original site). Dr DMASS+ is an improved version of Dr DMASS ( https://medals.jp/elist/detail/116.html ) to add (iii)(iv)."
	Data type	mass spectral data

FragmentAlign

[ Official site ] [ Show detail ]	Summary	"This program is a JAVA program which can align metabolite peaks from GC-MS analysis using retention time and MS fragmentation pattern information and also GUI-based edit the alignment. It can use NIST format or MassBase MST format text files to form the alignment. As edit functions, it contains add/delete function of peak in peak group, add/delete function of peak group, merge function of peaks and peak groups, etc. It can also annotate aligned peaks using pre-defined data library of MS fragmentation pattern of known metabolites. User can edit the data library. Resulting alignment can save as text file. Other programs (Microsoft Excel, etc) can use this output file for comparative and/or statistical analysis. Old version (Metabolometrisc) is downloadable."
	Data type	"Metabolite repression , mass spectra"

GRIFFIN

[ Official site ] [ Show detail ]	Summary	"It is a high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight. This system consists of two parts:1) HMM section using family specific multiple alignment of GPCRs, 2)SVM section using physico-chemical feature vectors in GPCR sequence."
	Data type	"Ptotein-sequence , amino acid sequence"

GRisk

[ Official site ] [ Show detail ]	Summary	Under investigation
	Data type	Under investigation

HEAT

[ Official site ] [ Show detail ]	Summary	"H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. This technique is called Gene Set Enrichment Analysis (GSEA), and is popularly used in analyzing results of microarray experiments. Fisher's exact probability is used in statistical tests of HEAT."
	Data type	Annotation

HapRisk

[ Official site ] [ Show detail ]	Summary	Under investigation
	Data type	Under investigation

Hyperlink Management System

[ Official site ] [ Show detail ]	Summary	"Hyperlink Management System is an original tool for setting hyperlinks to major databases related to human genes and proteins worldwide. For details, please refer to the document here (http://staff.aist.go.jp/t.imanishi/about_hms.html)."
	Data type	Data identifiers (IDs)

ID Converter System

[ Official site ] [ Show detail ]	Summary	"ID Converter System is an original tool for converting IDs used in major databases related to human genes and proteins worldwide. For details, please refer to the document here (http://staff.aist.go.jp/t.imanishi/about_hms.html)."
	Data type	Data identifiers (IDs)

ID Resolver

[ Official site ] [ Show detail ]	Summary	"ID Resolver is a tool for discriminating various types of data IDs. If you have any data IDs of unknown origin, please try it. Multiple IDs can be discriminated at a time."
	Data type	ID identifiers

KAGIANA

[ Official site ] [ Show detail ]	Summary	"We have developed the KAGIANA tool, which allows a user to retrieve summary information obtained from selective databases and to access pages for a gene of interest in those databases. The tool is based on Microsoft Excel and provides several macro programs for gene expression analyses. It can assist plant biologists in accessing omics information for plant biology. The KAGIANA tool is freely available at http://pmnedo.kazusa.or.jp/kagiana/(cited from the original site)."
	Data type	Gene expression

KaPPA-View

[ Official site ] [ Show detail ]	Summary	"The web-based tool KaPPA-View was developed for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. The presentation of data in this manner facilitates a good grasp of the transcripts and metabolites, leading to hypotheses of gene function in the metabolic pathway being examined. (cited from CiNii http://ci.nii.ac.jp/naid/110004822705/)New Features of KaPPA-View4:1. A comprehensive review of the system was conducted, and the processing speed was improved dramatically compared to the previous versions.2. As well as Windows, Mac OS X is now fully supported and you can use all the features on it.3. The users can use their own metabolic pathway maps for the analyses.4. As a function for the system developers, KaPPA-View4 offers features to display data directly from external systems such as databases and applications.(cited from original site http://kpv.kazusa.or.jp/kpv4/information/overview_en.html )"
	Data type	Metabolite repression Gene expression

KaPPA-View4 KEGG

[ Official site ] [ Show detail ]	Summary	"KaPPA-View4 is metabolic pathway database which is aimed to better understand metabolic regulation and to generate hypotheses from huge public available 'omics' data, i.e. transcriptome, metabolome, gene-to-gene co-expressions and metabolite-to-metabolite co-accumulations.KaPPA-View4 KEGG is one of the KaPPA-View4 version that has the pathway map data from the Kyoto Encylcopedia of Genes and Genomes (KEGG), and includes species infromation of animals, plants and microorganisms. Gene family maps generated from the ""Genes and Proteins""classification of KEGG BRITE are also available. (cited from original site)"
	Data type	Metabolite repression Pathway

LAMP

[ Official site ] [ Show detail ]	Summary	"LAMP is a code for multiple testing correction. Given the relationships between transcription factors (TFs) and genes and gene expression levels, the code lists up statistically significant combinations of TFs. The LAMP algorithm calibrates the Family-Wise Error Rate (FWER) at the same level of Bonferroni correction."
	Data type	p-values of multiple testing correltions

PMID-Extractor

[ Official site ] [ Show detail ]	Summary	"PMID-Extractor allows a user to obtain PubMed IDs (PMIDs) from PDF files or text format files of journal paper in your hand. From Digital Object Identifiers (DOIs, http://en.wikipedia.org/wiki/Digital_object_identifier) or text information (e.g. titles) in the first page of each files, To start using PubMedScan, a paper recommender, PMIDs are required to specify the users' interest. That is the main usage of PMID-Extractor. "
	Data type	Journal

PowerFT

[ Official site ] [ Show detail ]	Summary	"The peak detection and annotation tool for the analyses of metabolomics data obtained by chromatography - high resolution mass spectrometry(cited from original site).PowerFT is now available as a part of an integrated tool ""PowerGet""."
	Data type	mass spectrome data

PubMedScan

[ Official site ] [ Show detail ]	Summary	"PubMedScan is a automatic paper recommendation system for newly published PubMed papers that are related to your interest. This system has the following features: 1) queries are given by a list of PMIDs to search for related articles rather than by keywords or phrases; 2) related papers are reported daily by E-mail and stored in the system; 3) the similarity score between two articles are, currently, scored by PubMed ""Related articles"" service; and 4) the system can be used through either Web (ver 2.0) or software for local installation (ver 1.1). The local version can be installed on a UNIX machine such as Linux and Macintosh. PHP, MySQL, Apache and Perl modules are required. This system is key-word free, therefore effective to compensate for the keyword search in surveying the papers.To collect the PMIDs of your interest easily from your PDF or text files, we also provide software ""PMID-Exporactor""."
	Data type	Articles registered in PubMed

SAMURAI

[ Official site ] [ Show detail ]	Summary	Gene expression networks have different gene components depending on the cell types. SAMURAI is a tool for finding such minimal functional units of genes called modules from large-scale gene expression data. Modules are searched against by an ultra fast and exhaustive biclustering method using a closed itemset mining algorithm.suspending for relocation. (confirmation on 2012/11/05)
	Data type	Gene expression

SGCAL

[ Official site ] [ Show detail ]	Summary	"We have developed a web-based tool named SGCAL (Structural Glycomics CALculations). SGCAL is capable of building a 3D structure from oligosaccharide sequence information and of visualizing the calculated results and the experimental MS data, thereby supporting investigations on correlations between the structure of oligosaccharides and their fragmentation patterns. "
	Data type	Sugar chain

SNP-system

[ Official site ] [ Show detail ]	Summary	"We developed SNP-system which is unified in common interface and released it on the web.Website( http://www.h-invitational.jp/snps/ ) was closed, and at 22th Mar 2013, The archive opened in MEDALS Archive."
	Data type	DNA-sequence

SokanProject

[ Official site ] [ Show detail ]	Summary	This program is a JAVA program which calculates Pearson product-moment correlation coefficient from large matrix of numeric values by best-subset selection procedure with a parameter and outputs a result text file. It can calculate correlations of co-expressed genes or co-accumulated metabolite peaks from multiple experiments of microarray or non-targeted metabolome analysis. The resulting output file can apply to search functionally related gene or metabolite candidates of target gene or metabolite and correlation-based network analysis using other program or script. The program also can apply small-scale dataset.
	Data type	Gene expression

SpiceHIT

[ Official site ] [ Show detail ]	Summary	"This program is a JAVA program to detect metabolite peaks in CE-MS experimental data measured by SIM mode. It can use CSV text file as an input file. Peak list is calculated by parameters of peak width, peak intensity, etc with smoothing function. Metabolite name of targeted peaks is automatically characterized using definition file. In addition, user can edit the annotation of these and another unknown peaks by this program. The result can output as Excel format file that contains multiple sheets for each m/z value. This program can collect and summarize peak information, both of known and unknown metabolite, in a same manner. It can produce large-scale dataset for metabolome analysis.."
	Data type	Metabolite repression

THE MICROARRAY ANALYSIS SYSTEM - TREBAX -

[ Official site ] [ Show detail ]	Summary	"The Micro array analysis system TREBAX is a computersystem that makes possible the analysis and evaluation ofgenetic expression profiles, molecular biological function andeffective assignment of corresponding DNA nucleotides by mainlymanipulating data derived from spot type array methods (cDNAMicro array methods). Moreover, TREBAX can also be applied tothe analysis of any type of data other than cDNA micro array databy only modifying the respective input format.(Quoted from http://kanaya.naist.jp/Web/software/trebax/manual/Emanual.pdf)"
	Data type	Gene expression Microarray data

Web page checker

[ Official site ] [ Show detail ]	Summary	"A web page checker. This tool can monitor web pages, and grouping of web pages, highlight changes in a page, and send Email reports. "
	Data type	Web contents

Workflow

[ Official site ] [ Show detail ]	Summary	"A workflow can be defined as a series of jobs or an efficient framework which can be used for similar repeatable work.As a simple example, there is a series of jobs which can be defined as a workflow. First, find homologous proteins to the given protein, then create a phylogenetic tree using those protein sequences. To do this, we first need to perform BLAST and pick several sequences for multiple sequence alignment. If we defined this flow as a workflow, every job will quickly and smoothly be done.(cited from the original site). "
	Data type	workflow

Others ( 29 )