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ADMER2

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)

CADLIVE

Summary CADLIVE is a system for constructing large-scale biological networks (metabolic and gene regulatory networks) using GUI (Graphic User Interface) and saving them as regulator 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

Dr DMASS

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+

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 ( http://medals.jp/elist/detail/116 ) to add (iii)(iv).
Data type mass spectral data

GRIFFIN

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

HEAT

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

ID Converter System

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)

KAGIANA

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

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

PMID-Extractor

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 (http://medals.jp/pubmedscan/), a paper recommender, PMIDs are required to specify the users’ interest. That is the main usage of PMID-Extractor.
Data type Journal
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