INOH Pathway Database: Software Archives

March 10, 2011

INOH client application new version is available!

Our new INOH Client is now available.
Windows, Max OSX and Linux are supported.
JRE 6.0 is required.

You can download INOH client application from here.

The version number is updated from 3.4.0 to 3.5.3.

Release Notes

======================
Version 3.5.3

Newly added and improved features:
- improved the node and edge's SVGs.
- added Protein nodes (pink node, green node, orange node, purple node, and the phosphorylated and modified nodes of these nodes).
- improved "Erros" check.
The "Passing edge" was able to be pulled only between nodes of the same type.
- "Overview Area" and "Magnifier View Area" is fixed 100% zoom.

bug fixes:
- layout problem after the server search.

Posted by HiromiNakamura : 06:04 PM | TrackBacks

January 06, 2011

Similarity Search service of INOH client is available!!

We have developed a prototype web tool that accepts a graph query, whose nodes and edges are proteins and their relations respectively or "Event" and their connections respectively, searches the pathway/network data for the similar subgraphs on INOH.

This tool is designed on the assumption that a pathway/network query is submitted through the INOH client tool.

Please install the INOH client tool and the INOH pathway dataset from this site.

Usage:

In the INOH client,

0) Set your mail address to get the link URL of the results from "Tool" -> "Settings" -> "Similarity search" tab,

1) Open one of the INOH pathway diagrams.

2) Select a region of nodes and edges that you are interested in.

3) From menu, select "Search" -> "Similarity Search" -> "MoleculeRole Ontology" or "Event Ontology".

After that, your web browser will open and show the similarity-search page with your query.

And you will get the submit notice mail from INOH with access URL for your similarity-search page.

Posted by HiromiNakamura : 06:46 PM | TrackBacks

INOH client application new version is available!

Our new INOH Client is now available.
Windows, Max OSX and Linux are supported.
JRE 6.0 is required.

You can download INOH client application from here.

The version number is updated from 3.1.9 to 3.4.0.

Release Notes

======================
Version 3.4.0

Newly added and improved features:

- added "Similarity-search".
- added "Copy & Paste", "Up", and "Down" in "SequenceFeature edit" and "Evidence edit".
- added "ID search ( Node & Edge)".
- added "EC" in the XREF field become linkable.
- improved "Change node type" and "Change edge type" in "Object".
- enabled "Overview Area" and "Magnifier View Area" to close.
- "MoleculeRoleOntology" field is changed from Two or more input to singular input.
- improved "Erros" check.

bug fixes:
- "Use regular expression" in "Find local".

Posted by HiromiNakamura : 06:37 PM | TrackBacks

April 28, 2010

INOH client application new version is available!

Our new INOH Client is now available.
Windows, Max OSX and Linux are supported.
JRE 6.0 is required.

You can download INOH client application from here.

The version number is updated from 2.2.2 to 3.1.9.

Release Notes

======================
Version 3.1.9

Newly added features:

- added "Font" , specify the default font in "Tool --> Settings".
- added "Organism" , specify the default value of Organism property in "Tool --> Settings".
- added "Change node type" and "Change edge type" in "Object".

- added "Overview Area" and "Magnifier View Area".
The Overview Area is placed on the top right side of the screen.
Overview of the diagram you are currently editing is displayed in this area.
The Magnifier View Area is placed on the bottom right side of the screen.
Magnified view of the diagram you are currently editing is displayed in this area.

- added "Reduced View Mode".
The reduced view that focused on molecular transition in the normal view, and these modes can be easily switched back and forth.

Posted by HiromiNakamura : 03:07 PM | TrackBacks

May 14, 2009

INOH client application new version is available!

Our new INOH Client is now available.
Windows, Max OSX and Linux are supported.
JRE 6.0 is required.

You can download INOH client application from here.

The version number is updated from 2.0.2 to 2.2.2.

Release Notes

======================
Version 2.2.2

JRE 6 is required.

Newly added features:
- supported Mac OSX.
- bug fix in "Ontology viewer links".
- bug fix in "Check error".
- ServerURI changed.
http://www.inoh.org/axis/services/InohWebService
-->
http://www.inoh.org/axis2/services/InohWebService2

Posted by HiromiNakamura : 04:39 PM | TrackBacks

February 04, 2008

INOH client 2.0.2 Mac OSX support

INOH client 2.0.2 does not officially support Mac OSX because some of its features require Java 6, which has not been made available from Apple yet. But if you only do browsing then you can use the linux version on your mac. See detailes in the "more" section bellow.

INOH client is a pathway editor and a front end of our
database and Java 6 is required to issue a query.

But you can install the linux version on your Mac and browse pathways.
1. download Linux without Java VM from
http://www.inoh.org/Web_Installers/install.htm

2. run the downloaded installer by
# sh install.bin

4. cd to InohClient and edit the inoh.sh script in the bin-sample
a) edit the following two variables.
JAVA_HOME=...
INOH_CLIENT_HOME=...
b)edit the last line's ${JRE_HOME}/bin/java to fit your machine configuration.

5. start the INOH Client with
# sh inoh.sh

The pathway files (with .inoh extensions) are available from
http://www.inoh.org/download.html#PathwayData

Posted by KenFukuda : 06:48 PM | TrackBacks

October 25, 2007

Paxtools Level2 persistency layer available!

Paxtools persistency layer for BioPAX Level 2 specification is available from the BioPAX sourceforge CVS.

Paxtools is a Domain Object Model(DOM) for BioPAX, providing software tools such as editors, exporters, importers, visualization tools and analysis algorithms with an API for manipulating BioPAX models. The Paxtools core model is developed at CBIO, MSKCC and the persistency layer is developed by INOH database.

#NOTE: Currently we only have a "dev" version in the CVS.

[documents]
Find out here how to set up your Paxtools with a backbone DBMS.
The javadoc for the Paxtools Level2 persistency layer API is available here.
You can also get the pdf file of the paxtools poster abstract at ISMB 2007 here.

Paxtools provides a complete domain object model (DOM) in Java that enables users manipulating and evaluating BioPAX. It also provides state-of-the-art persistence services based on Java Persistence API. Finally Paxtools implement a fail-fast validation framework, mitigating the cost of potential pitfalls for the developers. Paxtools was designed to be modular, lightweight and platform independent to be easily embedded into applications.

[quoted from the ISMB2007 poster abstract]

Posted by KenFukuda : 10:47 AM | TrackBacks

May 12, 2006

INOH Client ver.1.0.6 released!!!

The latest INOH Client is Ver1.0.6

INOH Client Tool is a Java Application to edit and search our pathway data.

User's manual

Download

Release Notes
======================
Version 1.0.6
bug fixes in "Type" edit slot of "SequenceFeature"

Version 1.0.5
mouse-wheel support:
Scroll Wheel - Pan vertically
Ctrl+Scroll Wheel - Zoom

Posted by HiromiNakamura : 04:35 PM | TrackBacks

May 08, 2006

INOH Ontology Viewer Update (ver. 1.2.0)

INOH Ontology Viewer is an ontology browser for the INOH annotation ontologies.
ver. 1.2.0 allows XREF search by entering UniProt, KEGG, GO, SO IDs to see where your favorite term is located in out ontologies.

Release Note:
----------------------------------------------------------
1.2.0 UniProt,KEGG,GO,SO IDs in the XREF field become searchable

1.1.1 "synonym" is added to the default search configuration

1.1.0 added query string normalization for "-" and WORD UNIT, Phrase search

1.0.0 open to the public
----------------------------------------------------------

Posted by KenFukuda : 12:17 PM | TrackBacks

April 04, 2006

INOH Client ver.1.0.4 released!!!

The latest INOH Client is Ver1.0.4

INOH Client Tool is a Java Application to edit and search our pathway data.

User's manual

Download

Release Notes
======================
Version 1.0.4
Do not list duplicated results in "Participant match" for the category "Hit Diagrams" and "Hit Events"

Version 1.0.3
New category "Hit Diagrams" in the "Search result summary" of "Keyword search".
User manual included in Help menu.
Tool chips display Source/Target IDs of edges.
object-def.xml update
1.The default value of "Organism" attribute of "ChemicalSubstance" node is "".

Version 1.0.2
object-def.xml update
1.changed "DNACompound" node's attribute name "DNAOntology" to "GenomeSequenceOntology".
2.deleted "EventRelation" node "Organism" attribute

Version 1.0.1
port 8083 not required anymore, normal 80 port is OK.
for Mac OS X users: INOH client now supports Command + Q.
bug fix in "Detail information dialog"

Version 1.0.0
open to the public

Posted by HiromiNakamura : 01:34 PM | TrackBacks