LMU URS 2025 poster (March 12 review; March 17 printing; March 21 symposium)

[kdahlquist]

The LMU URS will be held on Friday, March 21. You all will be presenting a poster from 4:30-6:00 PM in the UH first floor atrium as part of the biology poster session.

Abstracts are due on Sunday, February 9, but we would prefer to have them approved and submitted by Friday, February 7 so that it can be done on a weekday and not pushed off until the weekend.

Our standard practice is to draft the abstract on the wiki and review during our meetings. Let's have a draft by our next meeting on Wednesday, January 29. We will review the final draft at our meeting on Wednesday, February 5. Make sure to look at the instructions for length of the abstract.

URS website: https://academics.lmu.edu/orca/symposium/

[kdahlquist]

Don't forget to draft your abstract for the LMU URS. We will be reviewing it in the meeting tomorrow.

[ceciliazaragoza]

Here is our first draft for the LMU URS abstract:

Propagating Protein-Protein Interaction Network Support into GRNsight 7.2, a Web Application for Visualizing Gene Regulatory Network Models

Ngoc K. Tran, Cecilia J. Zaragoza, A'Kaia Phelps, Amelie Dinh, Milka Zekarias, John David N. Dionisio, Kam D. Dahlquist

Department of Computer Science, Department of Biology, Loyola Marymount University, 1 LMU Drive, Los Angeles, CA 90045, USA

GRNsight is an open-source web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network consists of genes, transcription factors, and the regulatory connections between them, which govern the expression level of mRNA and protein from genes. GRNsight reads user-uploaded Microsoft Excel adjacency matrices or SIF files and automatically displays a graph. Users without their own data can use GRNsight's back-end PostgreSQL database to select a GRN based on the Saccharomyces Genome Database (SGD). We have continued to incorporate additional support for protein-protein physical interaction (PPI) networks so that users can display node coloring on a PPI with a choice of top or bottom datasets of expression data in the sidebar and the navigation bar. New graph functionality has been implemented that allows the user to restrict the graph to viewport so that users can drag, zoom, and move the graph of nodes with the nodes staying within the bounding box of the graph. The project’s CI/CD pipeline has been migrated from Travis CI to GitHub Actions, integrating workflows for automated builds, unit tests, and linting to streamline development processes and improve maintainability. Ongoing development efforts prioritize bug resolution, user interface enhancements, and improved documentation. In response to user needs, GRNsight is now positioned to comprehensively address GRNs and PPIs, offering a unified platform for visualizing diverse molecular interaction models. GRNsight is available at https://dondi.github.io/GRNsight/.

Word Count = 230

[dondi]

Some edits after review:

Database, Display, and DevOps Improvements for GRNsight 7.2, a Web Application for Visualizing Gene Regulatory and Protein-Protein Interaction Network Models

Ngoc K. Tran, Cecilia J. Zaragoza, A'Kaia Phelps, Amelie Dinh, Milka Zekarias, John David N. Dionisio, Kam D. Dahlquist

Department of Computer Science, Department of Biology, Loyola Marymount University, 1 LMU Drive, Los Angeles, CA 90045, USA

GRNsight is an open-source web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network consists of genes, transcription factors, and the regulatory connections between them, which govern the expression level of mRNA and protein from genes. GRNsight can now also display protein-protein physical interaction (PPI) networks. Whereas GRNs have directed edges, PPI networks have undirected edges to indicate protein binding. We have continued to integrate PPI networks so that users can display node coloring on a PPI with a choice of top or bottom datasets of expression data. GRNsight reads user-uploaded Microsoft Excel workbooks and automatically displays a graph. Users without their own data can use GRNsight's back-end PostgreSQL database to select a GRN or PPI based on yeast data from AllianceMine. Database loading scripts were ported to AllianceMine because YeastMine was discontinued. New graph functionality has been implemented that allows users to restrict the graph to viewport so that they can drag, zoom, and move the graph with the nodes staying within the application’s bounding box. On the DevOps side, the project’s continuous integration/development pipeline has been migrated from Travis CI to GitHub Actions, integrating workflows for automated builds, unit tests, and linting to streamline development processes and improve maintainability. Ongoing efforts prioritize bug resolution, user interface enhancements, and improved documentation. GRNsight is now positioned to comprehensively address GRNs and PPIs, offering a unified platform for visualizing diverse molecular interaction models. GRNsight is available at https://dondi.github.io/GRNsight/.

[dondi]

The abstract has been finalized and can be submitted by February 7; we can move on to the poster

[ceciliazaragoza]

Does this name and email information look good for everyone?

[ntran18]

Good for me!

[kdahlquist]

Please make sure to use middle initials for everyone. I believe everyone put them on the GRNsight people page.

[ceciliazaragoza]

I submitted the Abstract with everyone's middle initials included.

[ceciliazaragoza]

I just received notice that we were accepted into the LMU URS 😄.