MEDALS Tool catalog Others

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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)

CADLIVE

[ Official site ] [ Show detail ]	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

[ 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 ( http://medals.jp/elist/detail/116 ) 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

None [ Show detail ]	Summary
	Data type

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

NA [ Show detail ]	Summary
	Data type

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)