Explore Projects

VDB is a volumetric, sparse and hierarchical data structure which can be used for volumetric rendering, simulation and computational solid geometry (CSG). This project aims to add a VDB as a new entity for volumetric data into BRL-CAD. Additionally, the VDB structure would be used to render volumetric data with ray tracing.

<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>

<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>Newt is a free, web-based, open source viewer and editor for pathways in Systems Biological Graphical Notation (SBGN). It is written with a series of libraries and extensions based on Cytoscape.js with utmost customization in mind. The purpose of this project is to improve Newt editor so that it is much easier to use and many more people can benefit from it.</p>

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.

This project aims to integrate the JSON data schema (management-event-schema) into the FieldActivity R Shiny application, enabling it to read variable information from the schema and store management activity data in a compliant and flexible manner. Additionally, the project will address the challenge of storing multiple incidents for specific management cases, currently unsupported by the existing data structure.

OpenSCAD currently supports Windows development/build setup through 2 key ways: MSYS2 and MXE. A MSVC based build has instructions circa 2012, but with significant changes in project structure, and updated/new third party libraries and dependencies, it would be useful to work on adding modern MSVC build support for Windows. Currently, most CI builds use MSYS2 instructions, which has a Unix style build system. The benefits of adding support for MSVC builds include having executable and library outputs (.exe/.dll), vcpkg support for third party libraries OpenSCAD depends on, and support for parallel builds for speed.

<p>The project aims at creating and developing a usable, self-explanatory and distinct frontend user interface for BETYdb-YABA application that will be used for Metadata Upload such as sites and experimental data from a csv file. A simple and clear web interface will be developed through this project to guide users through the process for uploading metadata and for checking the correct format of data for BETYdb database.</p>

<p>Currently the PEcAn stack is distributed using the VM’s. The Aim is to replace the current VM distributions technique with the docker containers and Also to modularize it into smaller independent parts like PEcAn, Postgresql &amp; Bety so it will become easy to maintain. Also to add a Setup/Admin web UI so it can support many features like setup Unique machine id, Sync between the database, automatically update bety and PEcAn (Or notify user when new update available if this feature is turned off), Setup new instance etc.</p>

<p>In this project, we would be aiming to implement a python library for the GraphSpace RESTful APIs. Implementing such a library will be boon for the GraphSpace users as they can integrate it directly in their Python based applications. A well organized documentation will also be maintained. Furthermore, we plan to document the RESTful APIs themselves using RAML and also generate a test suite for testing the RESTful APIs documented in RAML.</p>

<p>My main idea is to implement a plugin manager for FreeCAD that will be used to install/remove/update plugins and other unofficial workbenches/modules/macros. Besides this project will make the life of the FreeCAD developers, workbench authors as well as the end-user easier.</p>

<p>This project involves the development of an open source database to enable the linked exploration of data in the platform, including energy demand, supply and technology data. Data in the HUES platform is highly diverse and rapidly growing. Currently, this data is stored in separate platform modules using different data structures and file formats, making it difficult to explore holistically. We will migrate this data using a tool Mongify to migrate database from MySQL to MongoDB. The development of server based scripts to automatically extract relevant data from the modules of the HUES platform, and write this data to a common database. In the new database everything can be retrieved in the form of JSON objects. The development of a web-based portal for querying, visualizing and downloading data will be the last part of the project development.</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>CentiScaPe is a Cytoscape application used to calculate a number of different node centralities of an optionally weighted network, both directed and undirected, as well as plot the results by using real and normalized values in different plots. Several centrality measures are available: degree, average shortest path, eccentricity, closeness, betweenness, centroid, stress, radiality, eigenvector, edge betweenness, bridging centrality, etc.</p> <p>This project aims to implement a brand new centrality measure based on Shannon entropy called Network Quantity Information. This measure aims to quantify the entropy of a given network, by firstly calculating the entropy of its nodes and edges which can then be observed as a type of centrality measure. Once all the node and edge centralities are obtained, we can derive from them the complexity of the whole network, which provides us not only with an interesting “one-value” description of the network, but also gives us the ability to compare multiple networks, or multiple parts of the same network.</p>

<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>

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.

<p>The project aims at creating and deploying a user friendly, interactive and accessible website for PEcAN Project. The following objectives will be accomplished after the successful completion of the project.</p> <ul> <li>Revamping the design of the PEcAn Project’s website and drawing wireframes (using figma ).</li> <li>Developing a Static SPA(Single Page Application) website using Docusaurus.</li> <li>Markdown Documentations will be integrated as web pages.</li> <li>Functionality for adding and editing documentation.</li> <li>Setup GitHub actions for continuous integration.</li> <li>Write detailed documentation for users and developers</li> </ul> <p>After accomplishing above tasks we would have a feature-rich, accessible website with a clean and elegant UI.</p>

This project addresses the current incompatibility of the Systems Biology Simulation Core Library (SBSCL) with modern computing architectures, specifically ARM-based processors. It restores its functionality on these newer hardware platforms. By creating a flexible, solver-agnostic abstraction layer, SBSCL will integrate a variety of linear optimization solvers, including both open-source (GLPK, CBC, SCIP) and commercial (CPLEX, Gurobi) options. The project also explores extending functionality with advanced constraint-based analysis methods, such as Flux Variability Analysis (FVA), further enhancing SBSCL’s analytical capabilities. Comprehensive validation, clear documentation, and example workflows will ensure easy use and broad adoption. Ultimately, these improvements will substantially enhance SBSCL’s usability, reproducibility, and overall user experience. As a result, researchers will spend less time on technical workarounds and more time focusing on biological questions.

<p>Implement a new Web Assembly compiler backend for Accord Project's smart contract language (Ergo). This will allow Accord Project users to deploy their contracts to any WASM platform or allow any WASM user to call Accord Project templates.</p>

<p>Improve the quality and reliability of the FEM Workbench of FreeCAD by introducing a extensive and consistent testing approach and developing a test suite covering the whole FEM module.</p>

<p>This project aims to update current web infrastructure of BRL-CAD organisation. Specifically: creating new main web site at ‘brlcad.org’ as a central hub of all BRL-CAD web products, improving and redesigning documentation.</p>

The main goal of this project is to add support for handling runtime exceptions in SPF that will improve SPF's performance on SV-COMP benchmarks. There are two main reasons why SPF is losing many points in runtime exception verification tasks. First, SPF is not systematically exploring execution paths where symbolic variables could lead to runtime exceptions like NullPointerException and StringIndexOutOfBoundsException, resulting in many incorrect false results where actual exceptions are not detected. Second, the SV-COMP execution script is lacking proper property detection and result classification for runtime exception scenarios. To address these problems, we should extended SPF to have additional choices that will explore potential runtime exception scenarios when symbolic variables could represent values that can raise them. To deal with this, we can analyze why SPF outputs wrong answers for certain verification tasks and fix them. This systematic approach to runtime exception path exploration will help fix SPF's behavior, improving its scores on SV-COMP benchmarks. This project extends the SPF branch, sv-comp.

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.