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<p>In this project, I will develop a tool in Cytoscape app ClusterMaker2 that helps implementing new clustering algorithms in the app from inside Cytoscape. Cytoscape is a widely used software in systems biology for analyzing large and complex networks. ClusterMaker provides a tool to detect communities within the networks using different algorithms. In order to make the implementation of new clustering algorithms in ClusterMaker, Cytoscape jobs package is utilized for executing the algorithms remotely.</p>

<p>The aim of this project is to implement a real-time comment/discussion and reaction system that will allow users to comment on graphs and discuss ideas with each other using the GraphSpace web interface.</p> <ol> <li>Design a user interface for creating comments and discussions: When visualizing a graph, this interface should allow users to add comments as a means to discuss or share ideas with their collaborators for a given graph, analogous to the way "Comments" on Google Docs allow users to discuss ideas on text documents. Being applicable to graphs, the comment system on GraphSpace should apply to nodes, edges, groups of nodes, and subgraphs, or even the entire graph. Comments can be applied only to a specific layout as well. There should be a way to mark comments as resolved.</li> <li>Develop a web service for real-time comments and discussions: We would like to implement real-time storage, querying, and recovery of comments and discussions.</li> <li>Develop a reaction system for both the comment/discussion system: We would like to implement a reaction tool like GitHub for both the comment/discussion system.</li> <li>Integrate the web service with the user interface.</li> </ol>

<p>The Projects goal is to use opencpu and cytoscape.js in order to remove the difficulty for Biologists to tackle with the hassles of using R code or cytoscape for enrichment analysis. This will be achieved by leveraging the opencpu RESTful services API to create an R package of our own and use opencpu to create an API and use it to generate the same plots one would generate while using cytoscape.</p>

<p>The goal of this project <strong>‘Diff for Graphs’</strong> is to implement a graph comparison functionality which will allow users to compare two or more graphs that are accessible by them. This includes graphs created by them, graphs shared with them by other users and all the public graphs. This project extends the work done in <strong>‘Git for graphs’</strong> project - which was a part of GSoC ‘18.</p>

This initiative focuses first on creating a Rust runtime platform for Concerto. Presently, Concerto's runtime logic resides in JavaScript and we use Node/Browser execution to conduct that logic, however; the logic is becoming more difficult to be reused as expected in other execution environments. The long term plan is to create a reusable Validation Core written in the Rust programming language which loads Concerto entity metamodels in JSON format, validates against the requested Concerto entity types based on the appropriate input metamodel and allows both access to the same validation core as a WASM module which is used from JavaScript executed environments, and also through a native interface for callers that are not executing using vanilla JavaScript.

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>InSilico is an extensible editor which can be used for manipulating and analyzing many different file types, SBML files in particular. The current implementation of InSilico has Maven Tycho and Eclipse PDE as its build system. The existing build systems will be replaced by Gradle. The goal of this project is to create a Gradle plugin that allows users to configure their OSGi application in easily understandable commands. Upon completion of this project developers will be able to complete all the above noted sub tasks by just interacting with the Gradle script. Also interacting with gradle script does NOT mean writing complex scripts but in fact will just include using of simple gradle command developed through this project. This in turn will encourage developers to create plugins and features for InSilico and making the job of developer and users easier !</p>

<p>As modern OpenSCAD usage has advanced, it now makes more extensive use of libraries consisting of many files, and the editor features have not kept pace with this more advanced workflow. The goal of this project will be to add different IDE-like features to the integrated text editor thus advancing its usage. This will make the editor more user-friendly and easier to handle large codes. Currently, the editor supports features like syntax highlighting, bracket matching, numbering of lines, besides others. I will work on implementing multi-file editing support to the editor and autocompletion of OpenSCAD keywords.</p>

JPF currently cannot fully analyze Java 17 programs that use sealed classes and records — two features now standard in modern Java. This project completes Java 17 support in jpf-core by fixing sealed class enforcement, adding full record support (classfile parsing, metadata storage, and execution), and producing a Java 17 audit document that maps all remaining gaps for future contributors. The work targets the java-17 branch and builds on an existing contribution to the codebase.

<p>This project aims to add improvements in the admin panel of openPIP that is used to upload data and files, post announcements and change global settings of installed instances. The project also requires work on the creation of an installation package and installation guide for the new users to follow. Ultimately, the project will prepare openPIP for publication.</p>

This project improves Manifold’s CI and benchmarking by adding missing determinism, sanitizer, and performance regression checks. I will implement a required cross-platform determinism check (Linux/macOS/Windows), add a dedicated ASan+UBSan CI lane for a curated `manifold_test` subset, and introduce PR benchmark regression checks (`base` vs `head`) with non-blocking warnings. I will also add a scheduled benchmark pipeline that publishes versioned history and define a noise-control policy so results stay reliable. The final deliverable includes an interactive benchmark dashboard that visualizes trends and regressions over time using the published benchmark data.

Java Path Finder (JPF), a specialized Java Virtual Machine for software verification, excels with Java 8 but faces challenges with modern features in Java 11 and 17, such as bootstrap methods (e.g., lambdas and string concatenation) and internal functions like toString() and hashCode() for records. My project seeks to address this by enhancing JPF to fully support Java 11 and 17. I will upgrade BootstrapMethodInfo to manage string concatenation effectively, refine INVOKEDYNAMIC execution to mirror the host JVM’s dynamic call site generation, and ensure internal functions operate correctly for new Java features. Drawing on OpenJDK research, I’ll implement these changes and validate them with thorough testing. Deliverables include full Java 17 support in JPF’s default branch, a comprehensive test suite for string concatenation and records and updated documentation. This work will modernize JPF, enabling it to verify advanced Java programs and strengthening its value to the verification community.

Currently, PEcAn packages are not available to download from CRAN, this makes it harder to install on systems since it requires the user to manually download all the PEcAn packages and their dependencies. Adding PEcAn packages to CRAN will not only make it easier to install but also easier to find and easier to use as standalone modules. This will require fixing warnings in the build process, removing unnecessary dependencies, splitting modules, refactoring code, adding tests, and removing test failures.

<h4>Description:</h4> <p>The aim of this project is is to develop a web interface for DoMo-Pred which can help to simplify the analysis of protein-protein interactions in yeast, or, if possible, in all kinds of organisms.Just upload or input pairs of protein IDs and run then the web interface will return the result and researcher can easily share the result with their colleagues and visualize the network of those interactions with significant scores. Also, the result after sort with significant scores can be used for performing other analysis.</p> <h4>Project details.</h4> <ul> <li>Users can upload PWMs and domain files (or use built-in data or their own trained data as well as input list of protein IDs) the application will call DoMo-Pred to analyze then return the result as a table.</li> <li>An easy to use admin tool for change built-in dataset,like uploading more PWMs and domains and add more organisms or to remove certain PWMs and domains.</li> <li>Sort the result by score after evaluation, then pick those interaction with significant scores (under user specified cutoff) which can be download and used to perform different analysis.</li> <li>Use Cytoscape.JS to visualize the network of those interactions with significant scores.</li> </ul>

This project aims to make contract execution easier by removing the need to write TypeScript logic for every template. Instead, it uses an LLM to understand the contract and execute it automatically. The system adds three modes—disabled, fallback, and force—so users can choose between normal typescript logic and LLM execution. It also includes proper validation and formatting to ensure correct outputs. The project will be tested on different real world templates and compared with existing logic to check accuracy and performance.

<p>LibreCAD V3 Beziers and File I/O Support project involves further development of the LibreCAD v3 Kernel and LibreCAD Software itself.</p> <p>LibreCAD at the moment is at very beginning stage of its development and lacks many features to be a robust kernel and a Solid Usable Software.</p> <p>LibreCAD v3 Evolution considers this issue and tends to implement 3 featues in this kernel.</p> <ol> <li>Input Output to the Drawing Files ( DXF Format )</li> <li>bezier implementation in kernel ( Quadratic )</li> <li>bezier splitting operation</li> <li>bezier bounding box</li> <li>bezier intersections</li> </ol>

This project is primarily focused on creating an interactive display of the carbon cycle forecast and data assimilation system of PEcAn. The main goal is to revive the site-specific R Shiny Forecasting and SDA dashboard that is no longer operational and broaden its scope to cover a larger number of sites. Additionally, the plan is to construct a new comprehensive dashboard that combines both SDA and Forecasting graphs. Moreover, the proposal also aims to establish an automated notification email system for the visualizations.

<p>I would like to implement the undo function into libged. This will be a significant feature addition to BRL-CAD, giving designers the option to revert any mistakes they have made. I would also like to implement the transaction based command system. This will help in avoiding corruption of files even if the process is interrupted by a keyboard interrupt or power failure midway through changes.</p>

<p>Cytoscape is a highly popular open source bioinformatics software platform for visualizing, analyzing, and publishing graphs or networks representing molecular interactions, gene expression, and other biological data. As a desktop platform, Cytoscape is one of the most successful open source projects in biology, and it is capable of integrating observational data from numerous sources.</p> <p>Currently, when users are working with a network of connected genes or proteins, they have to use external web tools to perform simple enrichment analyses, e.g., using g:Profiler. However, g:Profiler provides a web service interface, so it would be relatively simple to provide access to this same service from within Cytoscape. More advanced tools for enrichment already exist as Cytoscape apps, such as BiNGO and ClueGO. The goal to produce an app that could eventually be included in the core distribution of Cytoscape.</p>

<p>In BRL-CAD, some work has been done in order to optimize the ray-tracing process, with ray-intersection calculations implemented in OpenCL for several primitives, taking advantage of GPGPUs parallel mechanisms to render scenes in a faster way. I propose to continue the optimization of the ray-tracing in BRL-CAD, by implementing the CSG Boolean evaluation on the GPU using OpenCL.</p>

<p>This is my proposal to the project, improve DXF import and export for OpenSCAD. It includes a breif introduction of myself, project description and timeline for this project. The project description is consist of three part, preparation which selecting external library, Integrating which is for both import and export integration, testing which is for creating tests case and test output of import and export. The timeline is the development schedule throughout the summer. An alternative timeline is available as well. Changes might be made due to the discussion with the organization and potential mentor.</p>

<p>This proposal targets the “Elmer-Integration” project outlined in the “Google Summer of Code” article on the wiki (<a href="https://www.freecadweb.org/wiki/Google_Summer_of_Code" target="_blank">https://www.freecadweb.org/wiki/Google_Summer_of_Code</a>). The project aims at an extensive integration of the elmer multiphysics solver into the FEM workbench of FreeCAD.</p>

<p>This project intends to make several improvements to compmodelmatch platform which will improve its performance and also add features such as ORCID and OAuth2 API Integration which will result to improve the usability of the platform.</p>