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<p>Traversal-based graph algorithms are good at extracting “subgraphs of interest” when applied to large networks. However, applying known algorithms may not be enough every time to extract the useful information. Some specialized queries may be helpful in this sence to extract more useful or more specific information. Actually, these types of queries are already implemented inside the PATIKAweb software that is a result of the study done by Doğrusöz et al. in Java programming language. The aim of this project is to move these implementations into the common use of developers by making an extension to Cytoscape.js, which is a commonly used graph drawing library written in Javascript. Cytoscape.js already includes some basic graph traversal algorithms such as DFS, BFS, Dijkstra, Bellman-Ford, Kruskal etc., but I believe that these specialized queries will provide a good functionality to be used in not only in biological networks, but also in other types of networks. With the advantage of compound node support in Cytoscape.js, these specialized traversal algorithms will also be easily applied to the large networks with compound node content.</p>

<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>

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.

The SBOL-Utilities repository is a python library that provides many useful methods and utilities on top of the main PySBOL3 implementation of SBOL3. All the utilities created in the SBOL-Utilities repository follows the design choices and implementations as described in the various SEPs (SBOL Enhancement Protocols). Now, GenBank is another popular file format for storing sequences, DNA components, etc, just like SBOL. Currently, SBOL-Utilities supports conversion to GenBank from SBOL3, but only by having an intermediate SBOL2 conversion. What I seek to implement in this project is a way to directly convert SBOL3 to GenBank, without any intermediate file formats. The final goal is to have a set of test GenBank files generated from conversion and implement unit tests for the same.

<p>Newt supports the Process Description (PD) and the Activity Flow (AF) graphs of SBGN. However, there is no conversion between these two graphs in the Newt. PD is a detailed version of AF. Thus, from PD, AF can be obtained but not vice versa. There is already a library for converting PD to AF. The goal of this project is to host a service for this converter and then integrate it into Newt.</p>

Customized SSH Authentication Free Implementation of the Cloud-COPASI for UConn users: The project proposal aims to create a customized version of Cloud-COPASI that already has a predefined HPC pool connection which will be used by all registered users of this version of Cloud-COPASI. It will also implement a quota system to prevent abuse of computing resources. This will be accomplished by using a predefined SSH connection to the facility. Instead of user holding the private key and moving the public key to the remote submit node, the server holds a database of all remote nodes and for each node it creates a separate public and private key pair. The public key will be copied to the remote node. The private key would be saved on the server. Whenever an authenticated user tries to connect to a particular submit node in the HPC facility, the private key for that node will be fetched by the server and will be used to authenticate the user against that remote node and there will be no need for the user to configure and enter any private key at all. Thus there will be just one private key for all users of a particular submit node. Server will also keep a tally of all the users that are currently using the server's private key at the moment. This will help implement a quota system to ensure that the resources are not maxed out. Over the span of 12 weeks, a customized version of cloud COPASI will be produced that will provide an easy to use interface for UConn users to submit their jobs and get results in quick time.

<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>

Over the years, a vast collection of OpenSCAD libraries has been developed by the community. These libraries provide pre-written functions and modules that can significantly accelerate the development process by offering pre-built components for common design elements, gears, fasteners, and more. However, discovering and integrating these libraries remains challenging, especially for new users. Currently, OpenSCAD lacks a dedicated library manager. This project proposes a solution by creating a simple and user-friendly OpenSCAD Library Manager. This project aims to significantly enhance the workflow for OpenSCAD users, allowing them to focus on design and innovation while leveraging the power of reusable components.

<p>A Cicero extension for Microsoft Word will enable lawyers to write “Smart Legal Contracts” directly on the Word document itself. This will extend the usage of Accord Project templates to non-technical users as well. Thus, greatly expanding the accessibility to technology.</p>

<p>This project is to expand the list of Finite Element Method (FEM) examples currently present in FreeCAD by adding more examples. The target will be to create an example for each available constraint and each available analysis type or equation type.</p>

This project involves updating cyPlot(a Cytoscape app written in JAVA) which provides the ability to plot data through GUI or CyCommands/REST. CyPlot uses plotly.js to achieve plot related functions. CyPlot also customizes plotly.js and PlotlyEditor to suit the needs of CyPlot. It currently supports plots including heatmaps, violin plots, volcano plots, dot plots, line graphs, and scatter plots. The main goals of this project include: 1. Add Histogram as an additional plot type. 2. Implement log scales for scatter plot, line plot and histogram plot. 3. Support linear regression. 4. Updated user interface (UI)

<p>As a design repository for Synthetic Biology, SynBioHub facilitates the sharing and searching for information, combining data from a variety of sources. SynBioHub uses the Synthetic Biology Open Language (SBOL) an open source data standard that enables an information rich encoding of genetic information. To enable greater utility of the SynBioHub platform, it is necessary to extend its capability in a manner that will enhance its usability to genetic wet-lab workers, creating a better synergy between the digital and physical workflows. When creating or using genetic designs in the laboratory, experimentalists frequently want to interrogate the information for specific DNA ‘parts’ prior to using them. The annotation of a DNA sequence will define which strings of the DNA nucleotide sequence encode specific function. Being able to visualize the correlation of sequence to function is critical for experimentalists. Currently SynBioHub lacks a visualization tool that would enable this visualization. Addressing this will greatly enhance the usability of the platform by experimentalists and this will facilitate the integration of digital and physical workflows.</p>

<p>The project will aim to enhance the existing annotation capability and add another type of annotations like dimensions , labels and single or multiple lines notes the idea is to make all kinds of annotation share the same logic in entering the properties of annotation and the graphical representations and taking advantage of the existing primitives like lines and fonts to represent the annotation this will help to exploit the existing capabilities of these primitives like rotation and positioning .</p>

<p>The Testing Dashboard project aims to develop an easy-to-read dashboard with features like a status board to check which inputs are working and which are down so that it will be easy to monitor the tests’ results. On the backend, it will feature running the sandwiched integration tests on some appropriate schedule.</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>

<p>Nowadays, most floating point computations are performed in double precision – with a mantissa of 53 bits. Nevertheless, depending on the application we are using, it is preferable more precision, such as double extended – 64 bits – quadruple extended – 113 bits – or even more. The main goal of this project is to research how we can achieve such arbitrary precision on PRISM – by this, we mean the user should be able to choose the precision of each calculation – in order to provide a close approximation of exact solutions.</p>

<p>Implement two algorithms which have the ability to do dimensional reduction in cluster Network. Principal Coordinate Analysis and t-Distributed Stochastic Neighbor Embedding in clusterMaker2 which runs on Cytoscape software platform.</p>

The project would undertake the necessary code restructuring to facilitate OpenSCAD's transition to rendering with modern OpenGL. An important early step will be adding clear delineation between code paths that result in underlying calls to the two different rendering methods. This groundwork would then grow into developer-controlled flags that would enable the eventual deprecation of the legacy fixed-function calls. Part of the process will involve assessing the readability and testability of higher-level rendering classes and performing refactoring in line with guidance from other developers. Another key area of focus includes assessing and implementing any remaining workarounds needed to replicate the information exchanged between OpenCSG and the legacy rendering classes.

<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>

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

<p>Implementing following dimensionality reduction techniques and clustering algorithms to clusterMaker2: UMAP, t-SNE, PCA, PCoA, Louvain, Walktrap, Edge Betweenness, Surprise, DBSCAN, Spectral clustering and Self Organizing Map. This project is a continuation from last summer's clusterMaker2 project, when I implemented a feature that allows running the algorithms on a remote server. These algorithms that will be added will also use the remote feature.</p>

<p>Currently, PEcAn is not available in CRAN, this makes it harder to install on systems since it requires the user to download all code first and install it. Adding PEcAn packages to CRAN will not only make it easier to install but also easier to find and easier to use standalone modules. This will require fixing warnings in the build process, removing unnecessary dependencies, and potentially splitting modules.</p>