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<p>The aim of the project is to allow users to upload the data in form of files(.csv, data table, google sheets, etc.) to BETYdb. It will done by creating an interface which will provide logical workflow to guide the user through the process of uploading to BETYdb. Crawler are used to increase the knowledge base.</p>

<p>BRL-CAD has 2 geometry editor applications, MGED and Archer. They have been created a long time ago with the technology available at that time. The project aims to create a new application to encapsulate the tools and functions of BRL-CAD.</p>

<p>Security and Semantic bugs exist in software systems, and discovering them is time-consuming, complicated, and challenging. Several static and dynamic techniques are presented for discovering bugs. However, finding a bug is still a challenging topic. In this work, we investigate developing a prototype tool that uses the benefits of using the lightweight specification, fuzzing, and symbolic execution for discovering security and semantic bugs in an arbitrary Java program. This proposal aims to extend Badger, meaning both SPF and Kelinci, with the ability of handling both pre and postconditions using the runtime assertion checker of OpenJML with the lightweight specification. Also, using and extending <code>Debug.assume()'' and</code>Debug.assert()'' mechanisms in SPF that they work like precondition and postcondition, respectively.</p>

<p>I am interested in the project “Appstore for the Cytoscape App” with Alex Pico, Barry Demchak and Scooter Morris as its mentor. My goals for the summer will be to improve overall user experience, security as well as accessibility of the Cytoscape App store by implementing following major goals:</p> <ol> <li>Improving the user interface, particularly with respect to the search result display, redundancy in the search result, etc.</li> <li>Writing test script for the website, both unit test as well as integration test.</li> <li>Deploying the website on production server and Documentation.</li> <li>Removing the remaining bugs in the code.</li> <li>Web App implementation for viewing Cytoscape app store from within CyBrowser.</li> </ol>

openPIP is an open-source platform for hosting and visualizing protein-protein interaction (PPI) data. The current version is built on a PHP 5.6 / Symfony 2.8 stack that has reached end-of-life, making it difficult to maintain and extend. This project performs a complete rewrite of openPIP using modern web frameworks: a React single-page application frontend with Cytoscape.js for network visualization, a REST API backend (Python/Django REST Framework or Node.js/Express, to be finalized with the mentor), and a PostgreSQL database, all containerized with Docker. Key deliverables include: (1) a clean REST API replacing the 27 monolithic PHP controllers, (2) an enhanced data upload pipeline supporting PSI-MI TAB and CSV formats with drag-and-drop, real-time validation, and async processing, (3) a responsive React frontend with interactive search, network visualization, and an admin panel, (4) production-ready Docker Compose deployment, and (5) a data migration script for existing openPIP deployments (HuRI, YeRI). I have direct experience with the openPIP codebase, having created its deployment guide and migrated the platform from openpip.baderlab.org to openpip.usask.ca.

<p><strong>An application for users to access biological data extracted from biomedical literature.</strong></p> <p>Project Mentor <strong>Augustin Luna</strong></p> <h3>Objectives</h3> <ul> <li>Easy search capabilities for biomedical entities (e.g., genes, proteins, and chemicals) for a corpus of extracted entities and interactions </li> <li>Users will be able to see the articles that mention entities of interest in easy to interpret manner. </li> <li>Users will be able to view results in a tabulated format </li> <li>Computational users will have access to an API to retrieve results programmatically</li> <li>Use modern technologies for better browser compatibility, user access, and simplified maintenance </li> </ul> <h3>Project Phases</h3> <ol> <li>Planning and deciding our approach towards the project </li> <li>Deciding on data structures</li> <li>Creating schemas and GraphQL interface </li> <li>Generating Wireframes </li> <li>Linking backend and frontend </li> <li>Working on functionalities like search, filter </li> <li>Basic prototype expected to be ready by 23rd June</li> <li>Taking feedback from community and mentors</li> <li>Implementing features advised by community and mentors</li> <li>Deploying the project</li> <li>Working on making a pipeline to automate data addition from <strong>PubMed Central</strong>.</li> </ol>

<p>The goal of the project would be to add support for PSIMI-TAB format to the admin tools of the DV-IMPACT database and allow the upload and download of PPI network data in the same format. Currently, the data upload can only be performed by the database admin. The objective is to create registration and user profile system that allows users to register and upload their own data independently without the need of the database admin to be involved in the upload process.</p> <p>The summarized goals would be:</p> <ol> <li>Create registration and user profile system that allows users to register and upload their own data independently.</li> <li>Add support for PSIMI-TAB format to the admin tools of the DV-IMPACT database.</li> <li>Add download PPI networks in PSIMI-TAB format to the frontend of DV-IMPACT database.</li> </ol> <p>The Project fulfills all these issues by:</p> <ol> <li>Creating a User Profile system type forum.</li> <li>Allow users to register, upload and download domain-peptide PPI data in the specified format.</li> <li>Modify the DV-IMPACT database present in the server to handle the upload to the admin tools in PSIMI-TAB format.</li> </ol> <p>Link to the evaluation task: <a href="http://dvimpact.herokuapp.com/" target="_blank">http://dvimpact.herokuapp.com/</a></p> <p>Github Repo: <a href="https://github.com/jajodiaraghav/DV-IMPACT" target="_blank">https://github.com/jajodiaraghav/DV-IMPACT</a></p>

<p>The project is “Appstore for the CytoScape Apps” with Alex Pico, Barry Demchak and Scooter Morris as its mentor. The goals for the summer will be to improve overall user experience, security as well as accessibility of the Cytoscape App store by implementing following four major goals:</p> <ol> <li>Cytoscape App Store migration from Python 2.6, Django 1.4.5 to Python 3.X, Django version &gt;= 1.8: </li> <li>Implementing Reviews and comments feature for the Cytoscape apps, sending them simultaneously to the registered app authors via registered email.</li> <li>Web App implementation for viewing Cytoscape app store from within CyBrowser.</li> <li>Support for submitting, browsing, downloading R and Python scripts.</li> </ol> <p>Link to the project idea: <a href="https://github.com/nrnb/GoogleSummerOfCode/issues/122" target="_blank">https://github.com/nrnb/GoogleSummerOfCode/issues/122</a></p>

The project would allow the 3D viewport to support custom shaders for the render mode (F6). This requires retrieving the necessary uniforms and other shader input/outputs, then providing them to the program. Moreover, currently the GUI does not have options to allow the user to manage which shader is used, or add their own. My project would add these interface options to support shader management for the render by the user. Additionally, a set of default shaders could be included which the user could switch between.

The APAP MCP server currently routes every tool call through an internal HTTP loop back to its own Express server, adding unnecessary latency, making MCP handlers impossible to unit test, and discarding all HTTP error context behind generic error strings. The MCP layer has zero automated tests and no client-specific documentation beyond a basic setup guide. This project introduces a shared service layer that both MCP tools and REST routes call directly via Drizzle ORM, eliminating the HTTP round-trip. Structured error types replace generic strings with machine-readable codes and HTTP status preservation. Deliverables: 1. Shared service layer refactor with structured error types across all 8 MCP tool handlers 2. Four-tier test suite (unit, integration, contract, E2E) with 90%+ coverage enforced in GitHub Actions CI 3. Client-specific tutorials for Claude, ChatGPT, and MCP Inspector 4. Developer experience improvements: Docker Compose quickstart, Pino structured logging, /healthz endpoint, and updated CONTRIBUTING.md A working proof-of-concept implementing the core refactor with 53 tests and 98.55% statement coverage is already live at github.com/JayDS22/apap-mcp-poc.

<p>LibreCAD is a free Open Source CAD application for Windows, Apple and Linux. It allows industrial designers and graphics enthusiast to create CAD projects of the highest standard and precision. With this precision and standard comes the need of high quality and accelerated rendering to visualise a document. LibreCAD 3 was designed to have multiple rendering engines without major modifications to its core. Right now LibreCAD 3 uses Cairo for rendering. For users with high resolution screens, Cairo is not convenient because of a slowness, due to a bad integration with Qt and a missing caching system. At each frame when rendering is done the data is sent from CPU to GPU which is very inefficient. OpenGL has lower CPU overhead for draw calls and state changes and lets you take advantage of the GPU to render graphics on your device's screen and performance is excellent. The project consists of replacing Cairo with OpenGL in LibreCAD 3.To make a complete well abstracted OpenGL implementation with C++ for the rendering in LibreCAD.</p>

<p>Project aims to wrap BRL-CAD geometry primitives in python using ctypesgen and extending support to use python BRL-CAD on multiple operating systems. The current version of the project is unstable and very weak in terms of functionality available. This iteration of work would fix all the issues as mentioned verbosely in the proposal.</p>

<p>The JSBML library is a powerful Java library that gives the use a easy possibility to read, write and manipulate SBML files with Java. Because there are many different levels and versions of SBML and much more software which is using it, it is often needed to secure the quality of the interchanged data. SBML provides a well maintained specification for SBML files and even a online validator to approve your own documents. JSBML actually is using this online validator for his validation process. But that means JSBML software, which want to check their created or loaded files, need internet connection to do the test. This project is about implementing a completely new validation system to JSBML, written in pure Java. The main focus here lays on a easy usability and good modularity to support future levels and versions of SBML too.</p>

The goal of this project is to add new functionalities to Newt to be able to create biological maps in GPML format from scratch or edit existing ones. This will provide users to have a web-based alternative to PathVisio where they can easily create/edit GPML maps from any computer with Internet access. The functionalities to be added will also include access to WikiPathways, easy identifier mapping and data visualization etc., as in PathVisio.

clusterProfiler is an efficient package that provides a universal interface for gene functional annotation from a variety of resources and is extremely helpful in data manipulation and its visualization. The idea of integrating Pathway Commons, which is an aggregated database of molecular interactions of approximately 20 databases, brings in scope to analyze data and obtain better results. However, the data lies in GMT format due to which it requires additional functions to bind pathways with their name and gene. It is then saved in RDS format to feed the enricher() function to obtain an enrichResult object. We perform ORA and GSEA using some functions defined in R script on Pathway Commons data to support it in clusterProfiler. With the advent of a new technique ssGSEA (single sample Gene Set Enrichment Analysis) used to quantify the activity of a specific pathway or gene set in individual sample,for example, analyzing heterogeneous samples (tumor samples), integration of ssGSEA with clusterProfiler will help in better medical analyses. Thus, using packages like GSVA(Gene set variation analysis) and GenePattern we can calculate enrichment scores in permutations and support ssGSEA in clusterProfiler.

This project will develop an intelligent chat interface for CellMinerCDB, a cancer genomics database, using GraphRAG (Graph Retrieval-Augmented Generation) to enhance accessibility for researchers. The system will convert natural language queries into executable R code and leverage knowledge graphs to provide context-aware responses about complex relationships between drugs, genes, and cancer cell lines. Key deliverables include: (1) A data bridge connecting R's CellMinerCDB with Python; (2) A GraphRAG component that builds and queries knowledge graphs from cancer genomics data; (3) NDEx integration for network visualization and sharing; and (4) A natural language interface powered by PandasAI. This project extends previous work by adding knowledge graph capabilities, improving entity recognition for cancer genomics terminology, and enabling standardized network sharing through NDEx. The completed system will democratize access to complex cancer genomics data, promote reproducibility in research, and establish a foundation for natural language interfaces to biomedical databases.

<p>Newt is a web-based tool to analyze biological maps in standard formats such as PD and AF languages of SBGN, SBML, and SIF.</p> <p>This project aims to provide database support for Newt. SGBN maps stored on the database using Newt must be stored in an integrated manner ( i.e. fit like a puzzle with the existing database ).</p> <p>Furthermore, Newt must also provide the functionality to query the database for maps of interest, based on genes of interest using algorithms such as shortest path between entities, k-neighborhood, upstream/downstream of an entity, etc.</p>

This project is being proposed to redesign and update the official site for BRL-CAD, which will add more details to the site related to the organization. The project will be made using the latest technologies like React, Hugo, or other site generators. Another important aspect of the project would be to make this documentation on GitHub more accessible (https://github.com/BRL-CAD/brlcad-docs/).

<p>This project is to automate reinforcement process of slab and footing by using the Reinforcement Workbench in FreeCAD.</p>

String solving is an important feature of symbolic execution for successful security and correctness analysis. In Java Symbolic Pathfinder (SPF), a widely used Java symbolic executor, existing string solving integration lacks support for many string functions, including some frequently used ones. To improve SPF string solving, I will implement support for unhandled string functions based on functions that are already supported. For some functions looping on the input string, I will construct solver constraints by symbolically executing the implementation of those functions. As stretch goals, I also plan to add support to StringBuilder/StringBuffer and implement regex solver integration. The deliverable of this project is an SPF branch with most string functions supported, together with documentation and unit tests for newly supported functions.

Cytoscape Desktop Application serves as a powerful tool for network analysis and visualization. However, its layout options are limited compared to Cytoscape.js library. By developing a layout plugin, we aim to enrich the desktop application with additional layout algorithms available in Cytoscape.js, thereby providing users with a more comprehensive suite of tools for network visualization and analysis. Our plugin will integrate with the SyBLaRS web service. This integration will process the user data through SyBLaRS, a powerful layout and analysis tool, and seamlessly incorporate the results back into the Cytoscape Desktop Application. By leveraging SyBLaRS, we can access all Cytoscape.js layout algorithms without the need to implement their Java versions.

<p>The overall goal of the project is to create a Cytoscape app (CyGraphSpace) for syncing networks from Cytoscape to GraphSpace and vice-versa. Conceptually, the app will be similar to the CyNDEx app, which syncs Cytoscape networks with NDEx.</p> <p>Currently, users can sync between Cytoscape and GraphSpace manually by following the given steps: Cytoscape to GraphSpace: First, export a network and its accompanying style file in Cytoscape to JSON files. Then upload these JSON files to GraphSpace using its web interface. GraphSpace to Cytoscape: Download a graph’s JSON and style JSON files from GraphSpace and then import these files into Cytoscape.</p> <p>CyGraphSpace will allow users to upload graphs and their styles directly from Cytoscape to GraphSpace without manual intervention and saving of files thus enabling a Cytoscape user to seamlessly share their networks on the web via GraphSpace. A user can also quickly import GraphSpace graphs into Cytoscape, analyze them with other Cytoscape apps, possibly make modifications, and then re-upload them to GraphSpace. This project will also require creating a well-documented Java library that interfaces with the GraphSpace REST APIs.</p>

<p>The aim of the project is to enhance the representation of the wire frame views by adding annotations to the sketch.</p>