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SMARTS 3D
| Summary | Since it is necessary to grasp the structure of highly precise solution state for determining the absolute configuration of chiral drugs using Vibrational Circular Dichroism (VCD) Spectrum, for the purpose of verifying cumbersome structural analysis, We developed a program which describes applicable conformation of organic molecules by clicking operation and describes it by using python scripting language. 2D chemical structural formula can be easily searched for partial structure by SMARTS. Furthermore, it is possible to search 3D fragment structure with different molecules by incorporating the patented homology determination method (patent 5672596) into the program and combining it with SMARTS. |
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| Data type | Protein structure |
SNP-system
| 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. |
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| Data type | DNA-sequence |
SokanProject
| 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. |
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| Data type | Gene expression |
SpiceHIT
| 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.. |
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| Data type | Metabolite repression |
THE MICROARRAY ANALYSIS SYSTEM - TREBAX -
| 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) |
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| Data type | Gene expression Microarray data |
toxRank
| Summary | toxRnak is an application that displays a list of compounds with an expression profile similar to the expression pattern of the input gene group. Given a signature of query drug, toxRank computes the similarity with reference to expression profiles which are developed rank matrix data. It is possible to generate flexible rank matrix from genes that users consider important for hepatotoxicity and molecular panels obtained with toxBridge. |
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| Data type | - |
Web page checker
| 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. |
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| Data type | Web contents |
Workflow
| 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). |
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| Data type | workflow |
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