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A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions
Published on: July 11, 2017
A graphical approach to tracking and reporting target status in structural genomics
Xiaokang Pan1, Gary E Wesenberg, John L Markley
1Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
Journal of Structural and Functional Genomics
|February 1, 2008
Summary
Structural genomics projects use new software to visualize protein structure determination pipelines as graphs. This improves data management and reporting for collaborative research efforts.
Area of Science:
- Biochemistry
- Bioinformatics
- Structural Biology
Background:
- Structural genomics projects involve complex, multi-step processes for protein structure determination.
- Collaborative efforts in structural genomics face challenges in information integration and progress tracking across research groups.
- Existing Laboratory Information Management Systems (LIMS) may not intuitively display project progress.
Purpose of the Study:
- To develop a system for abstracting and visualizing the flow of targets through a structural genomics pipeline.
- To create software for generating specialized data reports for repositories like TargetDB and PepcDB.
- To improve inter-group communication and data accuracy within structural genomics projects.
Main Methods:
- Abstracting the structural genomics workflow as directed acyclic graphs or trees.
- Developing Perl CGI scripts integrated with Graphviz for a graphical web interface.
- Creating Perl-based software to transfer LIMS data into PepcDB-compatible XML reports.
Main Results:
- A software package was created to track protein structure determination progress.
- The software generates XML reports for TargetDB and PepcDB.
- Implementation facilitated inter-group communication and improved LIMS data quality and reporting efficiency.
Conclusions:
- Visualizing workflows as graphs enhances understanding and management of structural genomics projects.
- The developed software improves data integration, accuracy, and reporting for collaborative structural biology.
- This approach supports the data dissemination requirements of initiatives like the Protein Structure Initiative (PSI).
