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CellMinerCDB provides a web-based resource for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer cell line datasets (the NCI-60, Sanger/MGH GDSC, and Broad CCLE/CTRP).CellMinerCDB enables data queries for genomics analyses and exploration of pharmacogenomic determinants of response. It leverages overlaps of cell lines and drugs across databases to examine several biological questions. CellMinerCDB is built using R Shiny which provides a modular framework. This proposal is aiming towards adding an additional module in CellMinerCDB for Network Analysis that will provide an easier visualization of averaged genetic profiling data on top of a curated set of pathways.

<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>

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>We have to create a service for VCell users that allows Fiji/ImageJ scripting to directly access the VCell client. We have to expand this service into a series of user-friendly plugins for ImageJ that will automate processing and analyzing cell imaging simulation experiments.</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>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>

The objective of this project is to enhance the PEcAn Project by optimizing its modules for standalone use. Despite PEcAn's robust framework and its interconnected modules, there's a growing need to make these modules independently operable. This shift is essential to simplify module usage, testing, and development, making the system more accessible and efficient for users and contributors. The focus is on optimizing our modules for standalone use, enhancing their individual operability within PEcAn's interconnected framework with our top priority being to 're-loosen these couplings by revisiting the design and interface of PEcAn packages .'

The goal of this project is to update the Python codebase for Appleseed from Python 2 to Python 3 and update the PyQT code and GUI to PyQT6. This update is necessary to ensure that Appleseed continues to function correctly and avoid potential issues that may arise due to Python 2's deprecation. The project will include updating the Boost C++ Libraries to the latest version and ensuring compatibility with other dependencies, including OpenEXR, OIIO, Embree, and Qt. Updating Appleseed to Python 3 may affect some of its dependencies, including Boost, PySide/PyQT, PIL, and other Python dependencies. Overall, this project will help ensure the long-term sustainability of Appleseed by modernizing the codebase and improving the user experience.

<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>Tutorials serve as an invaluable way to familiarize oneself with new software. Cytoscape.js currently provides demos but lacks tutorials to tie together many ideas into a fully realized implementation. This project entails writing comprehensive but easy-to-understand tutorials which demonstrate the power of Cytoscape.js, both to those new to the project and to those wishing to tackle more ambitious projects with Cytoscape.js. I envision a set of tutorials moving from a level just beyond the demos, to a tutorial that details the creation of both mobile and web apps. Based on the current demos, I feel that there are enough examples of possible Cytoscape.js based webapps but each needs more documentation. There is very little guidance provided to new users as to why each demo works the way it does. To use a car metaphor, it seems like the demos are oriented more for going from 60 - 100 mph than 0-60. As mentioned in the provided description, each demo exhibits a single concept rather than tying them all together. Tutorials will tie together the disparate demos into more powerful (while still easy to understand) examples of Cytoscape.js</p>

<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>

<p>GraphSpace is an user-friendly web-based platform that collaborating research groups can utilize for storage, interaction, and network sharing. A GraphSpace user can import graphs created in Cytoscape, upload them through a REST API, interact with them by customizing and saving layouts, share them within and between groups of collaborators, search for different graphs, and organize them using tags. The goal of this project is to build a notification system for GraphSpace which will allow a user to track important activities on GraphSpace via notifications, the purpose being to keep users on par and current with their GraphSpace activity. In doing so, there will three type of notifications: Group, Owner and Watching.</p>

The goal of this project is to enhance the usability of Decorator Command Set (DCS) data by developing a utility/method to convert verbose, complex JSON formats into a more human readable YAML representation and back again. Currently, it is highly verbose to read, write, and edit DCS JSON files. The plan is to implement a converter that turns DCS JSON objects into a simple YAML format and back again. The new YAML will be less verbose and more readable, helping people work with DCS better. By the end, a fully integrated converter will be delivered, complete with tests and proper documentation.

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.

<p>The project aims at developing a feature wherein the template developers can sign the templates (to authenticate the source) they developed. The contracts derived from the templates can be then signed by the parties involved in the agreement (to authenticate the signatories).</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>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>Celluloid has gone through a lot of improvements since v0.13. This has somehow affected the performance. The aim of my project primarily is to create a benchmarking suite which will be used to tune performance optimizations. The benchmarking suite will cover all the features of Celluloid. Further I will create benchmarking suite for Reel.</p> <p>The value of this project is immense to the Celluloid community as it will help us refactor and improve the performance drastically before the 1.0 release of Celluloid.</p>

Accord Project Playground: Empowering Developers Through Interactive Learning Problem: The Accord Project offers powerful functionalities for smart legal contracts, but grasping these concepts can be challenging for developers with varying backgrounds. Existing documentation and resources may not provide an engaging and interactive learning experience. Solution: Proposing and developing a user-friendly Accord Project Playground. This web-based platform will provide an interactive environment for developers to experiment with Accord Project features through: Modern UI/UX Design: An intuitive and visually appealing interface that aligns with the Accord Project's branding. Interactive Code Samples: Live code editing and preview capabilities to demonstrate functionalities in a hands-on manner. Integrated Learning Resources: Comprehensive documentation, tutorials, and search functionality for efficient learning. Sample Management: Functionality to save and export user-created Accord Project code (specific format to be determined). Integration of Live Chat-Bot. Open-Source Principles: Adherence to open-source best practices for transparency, collaboration, and maintainability. Deliverables: * A fully functional Accord Project Playground website with interactive learning features. * Comprehensive documentation for the playground itself, including installation, setup, and usage guides. * A well-structured codebase with clear version control and adherence to coding standards. * A thriving contributor's community with a contributor's guide outlining participation procedures. Impact: By creating this Accord Project Playground, I aim to: * Lower the barrier to entry for developers interested in Accord Project technology. * Foster a more engaged and active Accord Project developer community. * Enhance the overall accessibility and user experience of the Accord Project.

<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>TOR-IBIN will be an online resource for gathering and storing published interface-based protein-protein interactions (PPI). TOR-IBIN aims to make these networks available in a central repository with a unified format. The web interface will have a comprehensive search functions and provide options to download the integrated data in standard formats. The interface will also have a visualization module to visualize PPI data as a network, annotated with features of the predicted PPIs using the Cytoscape.js network visualization library.</p>

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

An LLM-assisted, human-supervised pipeline to extract, interpret, and reconstruct agronomic and ecological experiment data from scientific papers into structured, BETYdb-compatible records. The system uses an intermediate representation (IR) with field-level provenance (extracted/inferred/unresolved), deterministic validation, and experimental reconstruction logic to ensure accuracy, consistency, and traceability, significantly reducing manual effort and improving data quality and scalability.