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SigmaCERF Technical Information

Introduction to the SigmaCERF System - Components - Installation - Back Up Procedure - Update Procedure - System Requirements

IT Architecture
The general architecture is based on the realities of life science research. Customizable components are joined through appropriate multi-tier systems to bring integrated content to the researcher's desktop.

Data Standards
We supports the use of public domain data models. We believe strongly in the creation of such data standards and are actively working with the Collaborative Electronic Notebook Systems Association and other groups to promote them.

Components
We components are defined by public APIs and public communication methods. Alternative implementations of component functionality allow different vendors to provide solutions that integrate with SigmaCERF frameworks.

Data Integration
One goal of data models such as BSML is to support data integration efforts through the use of federated queries and through support for XML-based cross-references and linking technologies.

Collaboration
The system architectures support a number of forms of collaboration, including multiple-user access to server-based data. Together, these technologies enable collaborators to participate in shared research efforts.

BSML
Our bioinformatics applications represent data in BSML, a public standard that was developed initially under NHGRI funding by Dr. Joseph Spitzner, CTO and Dr. Jeff Spitzner.

INTRODUCTION to the SigmaCERF System

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SigmaCERF is designed to support collaborative research efforts through use of the Electronic Lab Notebook and Scientific Content Management components, while at the same time minimizing the impact of the system on the organizations IT infrastructure. This document presents a high-level overview of the SigmaCERF system architecture. Portions of this document are derived from the SigmaCERF Architecture and Design White Paper, also available from SigmaCERF. The general architecture of SigmaCERF involves a multi-tier client/server design. The primary architecture is a three-tier web services model with:

  • Local client that may be web based or application based
  • Java servlet/Java Server Pages (JSP) and Enterprise JavaBean (EJB) middleware tier
  • Persistence tier containing both relational and object data stores

For performance reasons, SigmaCERF assumes that most clients are connected to the middleware tier by a high-speed LAN (Local Area Network). This architecture allows SigmaCERF to take advantage of higher speed data transmission capabilities. The primary SigmaCERF server provides the persistence mechanisms for storing objects of all types modeled in the SigmaCERF object hierarchy. The storage of native XML objects uses encodings that are based on public standards wherever possible. The base implementation of relational storage uses the MySql relational database manager, which is a widely accepted open source implementation. SigmaCERF assumes a distributed processing model for data retrieval and analytical services. Complex services are managed by an asynchronous service delivery platform that uses the J2EE Enterprise Java Bean (EJB) architecture. SigmaCERF provides an open architecture for the configuration of processing nodes that provide a variety of services. [top]


COMPONENTS

The components of the Standard SigmaCERF system are as follows:

1. SigmaCERF Client Application – A Java Swing application that runs locally on each users computer. SigmaCERF Runs natively on Windows 2000, XP, and Vista, as well as Mac OS X 10.4 or higher. Requires 250Mb hard drive space and 500Mb RAM minimum (1Gb RAM preferred)

2. SigmaCERF Server – Runs on the organizations own internal server (may also be a cloud based SAAS server arranged by SigmaCERF). Composed of several components, all of which are provided and installed by SigmaCERF:

a. Apache Tomcat – acts as the web services mediator between Client and Server

b. SigmaCERF SigmaCERF Web Application Archive (WAR) – the custom SigmaCERF code that carries out all of the operations involved in the Electronic Lab Notebook and Scientific Content Management components that comprise the SigmaCERF server. This is installed in the Apache Tomcat application.

c. MySql – the database component of the SigmaCERF Server. Stores all relational information as well as metadata and access information (usernames, logins, roles/ permissions). Note that other standard database applications are supported as well (see SigmaCERF Enterprise Upgrade, below).

d. Apache Lucene – the full-text indexer that scans all submitted files and indexes the contents for searching.

e. SigmaCERF Distributed File Storage System – provides storage for all resources submitted by users, in their native formats. The names of each resource are obfuscated and the appropriate lookups are stored in the database. Note – no user data files (e.g. Word or Excel or other format) are stored in the database instance; they are stored in this Filesystem in their native format.

SigmaCERF ENTERPRISE UPGRADE

In addition to the above components, the SigmaCERF Enterprise Upgrade includes support for Microsoft SQL as well as other standard databases (to replace the Standard SigmaCERF MySQL instance), as well as LDAP integration to the SigmaCERF Server. [top]


INSTALLATION

All installation is performed by trained SigmaCERF personnel. Representatives of the user organization are invited to observe all steps of the operation, including:

1. Database Setup – installation of the MySQL database and the specific SigmaCERF Schema. If the SigmaCERF Enterprise Upgrade is purchased this is superseded by your own pre-installed database, such as Microsoft SQL, with the SigmaCERF SigmaCERF database schema installed by trained SigmaCERF personnel.

2. Apache Tomcat Setup – installation of the Apache Tomcat service and the SigmaCERF Web Application Archive

3. Configuration – configuration of the Apache Tomcat to the database instance and filesystem.

4. Initial User Configuration – addition of user accounts and workgroups as well as organization-specific business policies.

More information on the SigmaCERF Installation procedure can be obtained directly from SigmaCERF Support. [top]


BACKUP PROCEDURE

The SigmaCERF server can easily be added to your organizations existing backup structure.

The application path for the Apache Tomcat, as well as the SigmaCERF Distributed File Storage System, are the two locations which must be backed up. In addition, the database instance (MySQL for Standard SigmaCERF or another database such as Microsoft

SQL for the SigmaCERF Enterprise Upgrade) should be configured to perform a database dump into the SigmaCERF Distributed File Storage System (in a unique folder). SigmaCERF recommends nightly incremental backups to your existing system, with off-site backups rolled into the plan. More information on SigmaCERF recommendations for backing up your SigmaCERF server can be obtained directly from SigmaCERF Support. [top]


UPDATE PROCEDURE

The SigmaCERF SigmaCERF system has been designed to be easily and quickly updated.

Updates are typically performed by trained SigmaCERF personnel. Typically an update consists of the following steps:

1. Shut down the SigmaCERF Server.

2. Delete the SigmaCERF Web Application Archive file (and associated SigmaCERF directory) from within the Apache Tomcat instance.

3. Drop in the new SigmaCERF Web Application Archive file.

4. Start up the SigmaCERF Server.

The Apache Tomcat application will unpack the SigmaCERF Web Application Archive file and create a new SigmaCERF directory to replace the one which had been deleted on the server.

When a client application connects to the server following an update, it will detect that new components are available and download them on demand. There is no need for IT support staff (or end users) to make any updates to the client applications. More information on SigmaCERF updates can be obtained directly from SigmaCERF Support. [top]



SYSTEM REQUIREMENTS

These requirements are current as of SigmaCERF 3.5:

Clients

Operating System:

  • Windows 2000 
  • Windows XP
  • Windows Vista
  • Mac OS X 10.4
  • Mac OS X 10.5
  • Mac OS X 10.6

Processor:

  • Pentium 4 at 1.5 GHz (Windows minimum)
  • Core 2 Duo 2.4 GHz (Windows recommended)
  • G5 at 1 GHz (Macintosh minimum)
  • Intel Mac (Macintosh recommended)

Memory:

  • 1 GB RAM (2 GB RAM recommended)

Hard Drive:

  • 1 GB free hard drive space (5+ GB free space recommended)

Server

Operating System:

  • Windows 2000 Server 
  • Windows 2003 Server
  • Windows Vista Business
  • Windows 2008 Server
  • Mac OS 10.5
  • Mac OS 10.6

Processor:

  • Intel Xeon Dual Core 1.8 GHz or higher processor (Windows)
  • Intel Mac Dual Core (recommended)

Memory:

  • 2 GB RAM (4+ is recommended)

Hard Drive:

  • 250 – 500 GB free hard drive space (amount of disk space depends on the amount of data stored in SigmaCERF)

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