Explore Projects

<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>

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>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>SBGNViz is a Cytoscape.js based library for viewing biological maps in Systems Biology Graphical Notation (SBGN) notation. ChiSE is a library based on SBGNViz to add editing facilities for construction of SBGN maps or modification of existing ones. The aim of this project is to design and implement new features for the ChiSE editor library as well as improving existing ones.</p>

<p>BRL-CAD's MGED search needs an -exec option - like the find command in UNIX - but that would mean low level library functions accessing the high-level Tcl interpreter in MGED. The solution is to provide the database search routine with a callback and a userdata pointer. My task is to add the callback logic, extend the parser, write the callback for MGED, extend the evaluation of search plans and write tests and documentation for all changes.</p>

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.

<p>Recently, metamorphic testing techniques have been applied with success in various fields to find domain-specific bugs, as presented in <a href="http://ieeexplore.ieee.org/document/7422146/" target="_blank">this survey</a>. One field yet to be explored is that of programming libraries, which comes with its own set of challenges. The existance of multiple libraries means we have a rich set of equivalence relations we can employ for metamorphic relations, allowing extensive testing using this approach. This project aims to explore the suitability of applying metamorphic testing to these math libraries and evaluate their reliability and correctness.</p>

<p>Ontologies are an integral part of our scientific progress. The ability to share common definitions is crucial to answering questions, thus, an updated and persistent ontology is important to invest in. This project will upgrade the current ontology tagging system of WikiPathways by utilising the recommender REST-API of BioPortal. The first part deals with fixing current data fetching mismatches, where tags are stored and fetched inconsistently. The second part of this project is implementing an intuitive tagging function to the process of creating a pathway, allowing the creator to fetch suggestions from BioPortal and add them with a couple of clicks. Lastly, the final part pertains promoting the quality of the tags by crowdsourcing the votes of visiting users.</p>

This project sets out to take the initial step in merging BRL-CAD's two in-development GUIs: "arbalest" and "qged". The primary objective is to transfer qged's sophisticated GED console, which works via low-level calls to BRL-CAD's core libraries (such as libged and librt), into arbalest, while preserving the application's distinctive clean and easy-to-scale architecture. To support this endeavor, I will also expand BRL-CAD's new lightweight, modular, object-oriented API, known as "MOOSE". In addition to these core tasks, I will tackle compatibility issues related to arbalest’s Qt widgets to ensure proper display across different OSs, as well as resolve various GUI-related bugs.

<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>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>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>

<p>FreeCAD is a general purpose 3D computer-aided engineering &amp; design program available for Windows, Mac, and Linux, and as a result it has a huge amount of complexity from dependencies and deployment. Using the systems engineering process of configuration management, I will help streamline the development and release processes for FreeCAD.</p>

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.

Gradle is a build automation tool known for its flexibility to build software. A build automation tool is used to automate the creation of applications. The building process includes compiling, linking, and packaging the code. The process becomes more consistent with the help of build automation tools. Currently, SymbolicPathFinder is using Ant as a build automation tool but the Gradle resolves all the issues faced by building tools like Maven and ANT. It is Well-Known to be highly customizable for different projects dealing with various technologies. We can customize the project according to the needs of the project. Gradle is popular for providing high-speed performance, nearly twice as fast as Maven. Gradle makes building common types of projects easy by adding layers of conventions and pre-built functionality through plugins. We can apply all those to enhance our SPF project. At the end of this project, we will get High performance, Build Scan, incremental build (that states it executes the tasks). Some steps to Implement this project : 1. Create Gradle build from scratch. 2. Restructuring of the project. 3. Implement a continuous integration (CI) pipeline. 4. Improve Junit Testing. 5. Update Documentation.

<p>Pathways are created by selecting certain genes and studies then displayed in the PathwayMapper tab in the cBioPortal. However, not every page in cBioPortal has a direct link to PathwayMapper hence making inferences from specific pages and reflecting the outcome to PathwayMapper is not straightforward. In order to overcome the struggle to interact between the pages and pathways, a PathwayMapper tab will be incorporated into Study View, Patient View, and Comparison pages. To test the implementations, I will deploy cBioPortal to Heroku so that I can test the code and ensure that it works in a remote server. PathwayMapper is used to construct pathways however pathways can become very complex and hard to understand as the data mounts. Some features are expected to be implemented in PathwayMapper to decrease the complexity of pathways and make it easy for users to draw conclusions. Features expected to be implemented are Expand-collapse operations, Hide-show operations, Filtering, Highlighting. For PathwayMapper editor features I will use functionalities that are already implemented in the Cytoscape.js. Bugs in Collaborative Mode will be fixed.</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.

<p>This project aims to add new features to ABioTrans Plus(GeneCloudOmics) that includes the direct import of gene expression data from Gene Expression Omnibus (GEO) databases, Machine learning-based analysis, creating a detailed report with the performed analysis with figures and data, and add more gene expression analysis methods e.g. Gene Set Enrichment Analysis (GSEA) and sample comparison analysis and plots. Also, provide Docker support and CI/CD pipeline.</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>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>

Microbial associations play a fundamental part in deciphering underlying mechanisms of microbial communities. A series of algorithms have been developed to retrieve such associations from taxa abundance data, however the outcome is usually tool-dependent and a large number of the retrieved associations may be spurious. microbetag is a co-occurrence network annotator aiming at increasing/decreasing the confidence level of the associations of such a network. However, being a command line tool, microbetag’s output is hard to interpret; its true potential can be revealed only by visualizing its findings so researchers can combine the retrieved annotations with their expertise to make further conclusions. Cytoscape Apps support additional features, e.g. new layouts, connection with databases etc, on Cytoscape, a well-established open source software platform for visualizing such interaction networks. Goal of this project is to develop a Cytoscape App providing a graphical interface for the microbetag tool.

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.

<p>The aim of the project is to Implement GeneMANIA in Julia to optimize netDx for high-performance computing.</p> <p>The current Java-based implementation of GeneMANIA scales poorly on compute clusters because of the interaction Java's memory management with the architecture of these systems. Removing this bottleneck would allow netDx to handle datasets on the order of 10K-100K patients, 100-1000X larger than the size of current datasets.</p> <p>Julia is a high-level programming language, with syntax similar to Matlab and Python. It provides efficient matrix representation and built-in parallel execution capabilities, making it better suited for high-performance computing (HPC). In addition to optimizing netDx for HPC, the network integration algorithm will be tuned for problems specific to netDx, such as having relatively fewer nodes and more networks.</p>