SUMMARY OF AVAILABLE SOFTWARE

Following is a list of software that is available to download from the Informatics Core. Buildable source code software may require Ant or Maven, pre-built packages contain readme files with other requirements (such as Tomcat):

Adaptive Data Management
The Addama (Adaptive Data Management) Integration Framework offers services with standardized interfaces for managing the entire lifecycle of data... [more with downloads]

Image Repository
The Image Repository is simple and flexible package for storing and retrieving image files from high-throughput light microscopy experiments... [more]
[download]

Synonym Service
The Synonym Service is a web service that allows matching of identifiers across disparate informatics data sources, such as Ensembl and GEO... [more]
[download]

SOAP Interoperability framework
The SOAP Interoperability Framework is a set of SOAP clients written in multiple programming languages against a curated WSDL... [more]
[download]

LSID Framework
The Informatics Core LSID project serves as an example for creating an LSID authority and client... [more]
[download]

jUDDI updater
The UDDI Updater is a Ruby On Rails application that allows web service authors to add and edit information about their web services... [more]
[download]

DETAILS OF AVAILBLE SOFTWARE

Adaptive Data Managment

The Addama (Adaptive Data Management) Integration Framework offers services with standardized interfaces for managing the entire lifecycle of data. RESTful web services (addama-rest) are used to provide data-access to open source implementations of the Java Content Repository (JCR) standard. These REST APIs offer Retrieval, Persistence, Search and Access Control over the resources stored within a distributed network of content repositories. The provided package uses Apache’s Jackrabbit implementation of the JCR standard and can be installed and run on a local system or server. A README is provided for setting up and starting the JCR. Note that all of the following tools require access to a running JCR.

Addama (Data Access)

Tools to view and browse the repository using Addama services are provided below. In order to use these, the REST/URI package must be installed on a web server (such as Apache Tomcat). Further documentation, including code examples, are provided within addama-docs.war file found in the first download.

• Addama implementation of a REST interface to access, create and edit information in a JCR repository. download here
• JCR Browsing provided in the addama-html.war file. This tool allows a user to view and (limitedly) edit the repository structure. download here
• Access components. A java client is provided (with source). Clients for R, Perl, Python, Ruby and Matlab will be added as available. download here

Data Loader

These utilities provide the ability to load data into a JCR instance. The file loader allows a user to load single files from a local machine into a JCR running either locally or on a separate server. The batch loader loads all subdirectories and files from a local machine into a local or remote JCR instance. Please see the README file for details.

• File loader utility for loading file data directly into a JCR instance using XPATH information to define location. download here
• Batch loader utility for recursively loading all directories and files into a JCR instance. Metadata may be defined and loaded from tab-delimited text files. download here

Image Repository

The Image Repository is simple and flexible package for storing and retrieving image files from high-throughput light microscopy experiments. It is written in Java and features a web-service based front end for submission of large batches of images, a configurable input pipeline for metadata extraction and conversion to the TIFF file format, as well as a content repository that stores the original files, converted files and metadata in combination of the file system and a MySQL database. It also features a simple job control and fault tolerance mechanism.

The Image Repository provides a SOAP interface for uploading image projects. To meet requirements specific to the ISB Imaging Core, a web submission form was created that allows users to upload their imaging projects with any metadata and imaging files.

Because of the number and size of the files involved, the image repository uses a pull model, which allows loads to be monitored (and alarmed on), so that capacity problems can be addressed before the submission failures that would normally be encountered with a standard HTTP POST submission mechanism or something similar.

A repository navigation tool created in Rails allows a user to browse their projects and images as well as search for projects or images by metadata or free text.

This software has been built and tested using Java, Apache Axis2 1.2, Apache Tomcat 6 and Apache Ant. A MySQL database is also required. A readme file is provided to describe how to set up the database and build the repository. A test client and data are also provided and descriptions for use are also in the readme.

This package is currently in alpha, but under active developement.

download here

Synonym Service

The Synonym Service is a web service that allows matching of identifiers across disparate informatics data sources, such as Ensembl and GEO. It is written in Java and includes two separate packages. The SynonymAdmin tool to create the database and add data must be set up before trying to run the SynonymService SOAP server. Maven 2 is required to build these packages. A MySQL database, a servlet container (e.g. Apache Tomcat) and Apache Axis2 1.2 are also required. Please refer to the readme files for instructions on building, deploying and using the service.

The Synonym Administration tool provides basic administrative tools to the Synonym Service including adding and deleting mappings on any of the synonym databases that are currently hosted by the service

download here

SOAP Interoperability framework

The SOAP Interoperability Framework is a set of SOAP clients written in multiple programming languages against a curated WSDL. It was created to explore the scalability of Web Services in a multi-language environment.

The WSDL is written using document-literal encoding and has methods that return both simple types and complex types and examples of a SOAP server written in Java, C# and Perl.  Example clients are also provided in Java, C#, Perl and Ruby.  Apache Ant is required to build this project.  See the tutorial to create a server/client.

Example of a SOAP client written against the Synonym Service WSDL in C#

download here

LSID Framework

The Informatics Core LSID project serves as an example for creating an LSID authority and client. In org.systemsbiology.lsid.helloworld see the HelloWorldAuthority, HelloWorldDataService and HelloWorldMetadata service for an example LSID server.  An example client is provided in org.systemsbiology.lsid.client and a test case usage is in the SimpleClient class. 

LSIDs are used internally both in the content repository that is under development and to locate data within SBEAMS, the Systems Biology Experiment Analysis Management System. In this case LSIDs are assigned through a proxy service to data and metadata stored within SBEAMS allowing retrieval to occur through the LSID authority as well as the normal download channels of SBEAMS.  If you are interested in SBEAMS and the LSID proxy please contact us.

download here

JUDDI updater

The UDDI Updater is basically a web front-end to the database of JUDDI, an open source Java implementation of the Universal Description, Discovery, and Integration (UDDI) specification for Web Services.

download here

Also see new things that we are working on here.