Source: UNIV OF WISCONSIN submitted to
SESAME LIMS
Sponsoring Institution
State Agricultural Experiment Station
Project Status
TERMINATED
Funding Source
STATE
Reporting Frequency
Annual
Accession No.
0213000
Grant No.
(N/A)
Project No.
WIS01305
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2007
Project End Date
Sep 30, 2012
Grant Year
(N/A)
Project Director
Zolnai, Z.
Recipient Organization
UNIV OF WISCONSIN
21 N PARK ST STE 6401
MADISON,WI 53715-1218
Performing Department
BIOCHEMISTRY
Non Technical Summary
Data management has been identified as a crucial issue in all large scale experimental projects. In this type of project, many different persons manipulate multiple objects in different locations; thus, unless complete and accurate records are maintained, it is extremely difficult to understand exactly what has been done, when it was done, who did it, and what exact protocol was used. All of this information is essential for use in publications, for reusing successful protocols, for determining why a target has failed, and for validating and optimizing protocols. Although data management solutions have been in place for certain focused activities, for example genome sequencing and microarray experiments, they are just emerging for more widespread projects, such as structural genomics, metabolomics, and systems biology as a whole. The overall aims of the Sesame project have been to develop a LIMS that (1) provides a flexible resource for storing, recovering and disseminating data that fits well in a research environment (multiple views of data and parameters), (2) allows the world wide community of scientists to utilize the system, (3) allows remote collaborations at all stages, (4) provides full user data access security and data storage security, (5) permits data mining exercises and analysis of laboratory operations to identify best practices, and (6) simplifies the dissemination, installation, maintenance, and interoperability of software.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
50%
Developmental
50%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
90372991000100%
Knowledge Area
903 - Communication, Education, and Information Delivery;

Subject Of Investigation
7299 - Research equipment and methods, general/other;

Field Of Science
1000 - Biochemistry and biophysics;
Goals / Objectives
Sesame is a versatile Web-based laboratory information management system developed at the University of Wisconsin-Madison that is in use in multiple laboratories around the world both for small-scale and large-scale applications. Sesame supports the gathering, organization, processing, and analysis of information from a variety of sources, including databases, bench scientists, laboratory instrumentation, and software packages. Sesame has proved its value in structural and functional proteomics investigations, in the management of shared instrumentation centers such as NMR spectroscopy resources and molecular interaction facilities. The Sesame system enables collaborators to participate in a research project, with equivalent access to information and the ability to enter results and process data irrespective of location (given Web access). The requested funds will be used to support the continued development, evaluation, and testing of the Sesame software package. The software development will be aimed at (1) improving the efficiency and flexibility of the Sesame framework, (2) making it easier for users to customize the software for their own needs, (3) improving existing applications, and (4) developing additional applications. The goals are to make the software available to a larger clientele of structural biologists, molecular biologists, and biochemists.
Project Methods
The Sesame software is written in Java, uses CORBA as a middleware and is interfaced to a relational database management system. As part of this effort, we will create universal objects for developers so that they can develop Sesame modules to solve problems specific to their laboratory. We will ensure that the software runs on a variety of platforms, supports a variety of relational database management systems, and is firewall friendly. We will improve the documentation of the software, continue development of web-accessible user help pages, and create Sesame interfaces to a wider range of laboratory instrumentation. The schema and controlled vocabularies developed for various Sesame applications will be made available on the web to interested users. We will extend protocols for importing data from and exporting data to external data repositories. All software will be open-source.

Progress 10/01/07 to 09/30/12

Outputs
OUTPUTS: There have been 11 deployments over the last year, 2 of those major. The details are in the release notes on the Sesame website, http://www.sesame.wisc.edu. The Sesame instance in Madison, and the other instances we maintain, had no unplanned downtime over the last year. (So far, in 11 years, Sesame never crashed.) The only downtimes were for OS and Sesame upgrades, totaling about a day. The users have been only affected by network outages, that can happen between the client and the server. The New York Consortium on Membrane Protein Structure (NYCOMPS) Sesame instance from a server at the Columbia University to a new server at the New York Structural Biology Center (NYSBC), that is also used by the Cryo-electron Microscope Facility. PARTICIPANTS: Zsolt Zolnai - PI TARGET AUDIENCES: Sesame is a versatile Laboratory Information Management System for small scale and large scale structural and functional proteomics and metabolomics applications. It is actively used for day-to-day project management and data mining at high throughput structural genomics centers, shared instrumentation facilities and academic laboratories with diverse activities. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
150 new users (the total at the moment is 1699) were registered at the Madison instance during the last year. Parts of the Great Lakes Bioenergy Research Center (GLBRC) have started to use the Sesame instance in Madison. (The instructions are posted at the Sesame website, http://www.sesame.wisc.edu.) As always, Sesame is freely available, and one can use our instance at Madison, or install their own. Sesame is actively used at multiople PSI:Biology centers, at NMRFAM, and by many academic labs with diverse activities in the US and Worldwide.

Publications

  • No publications reported this period


Progress 08/01/08 to 07/31/09

Outputs
OUTPUTS: There have been 8 deployments over the last year, 3 of those major. The details are in the release notes on the Sesame website, http://www.sesame.wisc.edu. The Sesame instance in Madison had no unplanned downtime over the last year. (So far, in 10 years, Sesame never crashed.) The only downtimes were for OS and Sesame upgrades, totaling less than a day. The two Sesame instances installed last year at MCW in Milwaukee, and at NYCOMPS, in New York City, also had no unplanned downtime. Users have been, however, affected, by network outages at different places. A new Sesame instance has been installed at AECOM in Bronx. The installation and the upgrades were carried out using the instructions from our website, and without our assistance. As always, Sesame is freely available, and one can use our instance at Madison, or install their own. PARTICIPANTS: Zsolt Zolnai - PI TARGET AUDIENCES: Sesame is a versatile Laboratory Information Management System for small scale and large scale structural and functional proteomics and metabolomics applications. It is actively used for day-to-day project management and data mining at high throughput structural genomics centers, shared instrumentation facilities and academic laboratories with diverse activities. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
131 new users (the total at the moment is 1549) were registered at the Madison instance during the last year. Sesame is freely available, and one can use our instance at Madison, or install their own. (The instructions are posted at the Sesame website, http://www.sesame.wisc.edu.) Sesame is actively used at CESG (www.uwstructuralgenomics.org) and NYCOMPS (www.nycomps.org) PSI-2 centers, at NMRFAM (www.nmrfam.wisc.edu) and many academic labs with diverse activities in the US and Worldwide.

Publications

  • No publications reported this period


Progress 09/01/07 to 07/31/08

Outputs
OUTPUTS: There have been 14 deployments over the last year. The release notes with all the details are on the Sesame website, www.sesame.wisc.edu. Sesame has been made Java 1.6 compliant. Java 1.5 is still supported, but the support for older versions has been stopped. Both the client and the server side of Sesame will run on any platform that has JRE 1.5 or JRE 1.6 installed. The server side has been modified to support Oracle 10g. At the moment, the databases supported are: Oracle 10g (all editions, including the free 10g Express Edition), PostgreSQL 8+ and Microsoft SQL Server 2005. At least one RDBMS is available for every major operating system. The Sesame instance in Madison had no unplanned downtime over the last year. The only downtimes were for OS and Sesame upgrades, totaling less than a day. The Sesame website has been revamped, and many new pages were added. The instructions for installing a Sesame instance are also among them, and new help pages are added regularly. As it is a work in progress, some of the pages are still "under construction." The PI has given Sesame talks at NYCOMPS, NYSBC and AECOM, and held Sesame workshops at NYCOMPS and AECOM. PARTICIPANTS: Zsolt Zolnai - PI TARGET AUDIENCES: Sesame is a versatile Laboratory Information Management System for small scale and large scale structural and functional proteomics and metabolomics applications. It is actively used for day-to-day project management and data mining at high throughput structural genomics centers, national facilities and academic laboratories with diverse activities. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
124 new users were registered at the Madison instance during this reporting period. (The total number of users was 1418 on 07/31/2008.) Two new Sesame instances have been installed: one at MCW in Milwaukee, and the other at NYCOMPS, a PSI-2 center, in New York City. All the MCW's data has been moved from the Madison instance to their instance. Sesame is freely available, and one can use our instance at Madison, or install their own. Sesame is actively used at CESG (www.uwstructuralgenomics.org) and NYCOMPS (www.nycomps.org) PSI-2 centers, at NMRFAM (www.nmrfam.wisc.edu) and many academic labs with diverse activities in the US and Worldwide.

Publications

  • No publications reported this period