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<p>The goal of this project is to develop a model that can visualize biological networks as logic gate circuits, and vice-versa. In recent years, discrete dynamic modeling has emerged as a powerful method of modeling and understanding biological systems. One type, boolean network models (which was initially used as a prototypical model of genetic regulatory networks), has been shown to be a tractable approach for modeling large-systems. A boolean network consists of a set of nodes whose state is binary and is determined only by other nodes in the network through Boolean functions. The simplicity and self-containment of these graphs makes it extremely fast to simulate these systems and is also a very realistic interpretation of how biological networks actually work. Unfortunately, no libraries yet exist for converting a visualization of a biological network into a logic gate visualization and vice-versa.</p> <p>Thus, the aim of this GSoC project is to develop a web-based tool that can visualize biological networks, and also transform these networks into a logic gate-based system.</p>

<p>The goal of this project is to implement the support for Research Object specification into Nextflow workflow framework, with the aim to improve the reproducibility and transparency of the resulting data-analysis and computational workflows based on such tool.</p>

<p>OpenMS is an open-source software C++ library for mass spectrometry (MS) data management and analyses. A common task in proteomics is to identify and quantify proteins in complex biological mixtures. In a standard tandem mass spectrometry (MS/MS) protocol, a crucial part is to control the uncertainty in peptide identifications generated by search engines that match MS spectra to peptides. Based on an idea suggested by the OpenMS team, I propose a project to improve the posterior error probability estimation for peptide search engine results in OpenMS.</p>

Plone has the workflow manager from the starting version and it is also the biggest selling point for the Plone. We already have the backend implementatoin of Workflow manager in Plone but our new frontend which is Volto don't have this feature. After this project we can now build the workflow directly from the volto using diagram which is not possible in the Plone.

<p>This project aims to create a Markdown processor written in Ceylon that will be a part of the Ceylon SDK. This will be based mainly on the CommonMark spec. This will be a useful module since Ceylon already uses markdown in <code>ceylon doc</code> for documentation.</p>

The project aims to incorporate AI features into Template Playground to facilitate the creation of Templates and Concerto models. The ability to generate Accord Project Templates from user submitted text will be implemented. Users will be able to chat with their chosen LLM and get an understanding of how the whole ecosystem of Accord Project works in tandem to produce agreements. The editors in Template Playground will be enhanced with the ability of providing AI powered inline suggestions.

<p>I will work to find WebAssembly based solution for missing mediaRecorder API for browsers like Safari and Edge. By using native mp3 encoder that will be used in the browser with the help of Emscripten compiled javascript output.</p>

<p>The Moira API microservice serves as the backend for the web UI and it would be nice if the engineers who use Moira are able able to automate routine operations such as managing triggers with tools like Ansible. However, the API is undocumented currently and they have to study Moira’s source code or inspect the network requests from the web client to know the network requests they have to make and the responses to expect.</p> <p>As part of the 2020 Google Summer of Code, I wish to:</p> <ul> <li>Develop an up-to-date OpenAPI/Swagger description of the endpoints exposed by the API.</li> <li>Generate language-specific client libraries from the API description file - with special focus on a Golang client.</li> <li>Setup automated contract tests to test the OpenAPI document against the actual implementation.</li> </ul>

<p>Ordinary differential equations are widely used for modelling biological networks and processes of kinetics. The idea of the project is to create a web application that allows a user to submit an SBML model and select methods of analysis and receive results. The different kind of analysis methods that will be available for use are Steady State Analysis, Parameter Fitting, Simulation.</p>

<p>Abstract: plone.org is the main website of the Plone community where all the generic addons, plone releases and hotfixes are listed. Currently, there is no useful add-on listing and the process of updating the listings is not optimal. The goal of this project is to create functional prototypes of add-ons to: 1) display a useful listing for addons. 2) automate the process of updating plone.org with new add-ons, releases and hotfixes. 3) notify the user (Site admin) with information about vulnerabilities and available updates.</p>

<p>The goal of this project is to improve performance and provide more necessary features for Casbin.NET.</p>

<p>The​ support for Python 2 will be dropped in the coming years and thus it is important to switch to Python 3. There is a need to make sugar-toolkit and activities compatible with Python 3, to ensure the smooth functioning of the sugar activities in the future. The aim of this project is to boost this necessity.</p> <h5>Target</h5> <p>Following are the targets of this project:-</p> <ul> <li>To port all static telepathy bindings to TelepathyGLib.</li> <li>Make activity-chooser window modal.</li> <li>Make sugar-toolkit compatible with both Python 2 and Python 3.</li> <li>Make sugar-desktop compatible with Python 3.</li> <li>Port sugar-activities to Python 3 and make a release.</li> <li>Write the necessary documentation.</li> </ul>

<p>The aim is to increase the test coverage around the backend rails api codebase. Right now it has around 45% coverage. I aim to improve it by making the unit test coverage at least 85+ and also write integration tests using RSpec and Capybara. I also plan to start on the Rails Upgrade once the test suite is up and running.I plan to go one directory after the other and gradually covering the whole codebase to have a good test coverage.</p>

Sugar has a lot of activities, with 250+ on GitHub, and more elsewhere. These have scope for improvement; bugs, features, updated human translations, and release. This project will involve working on at least 12 activities to improve them.

<p>Constraint-Based Reconstruction and Analysis (COBRA) methods for Genome-wide Metabolic Networks (GEMs) have proven to be essential for the varied applications of metabolic modelling, from predicting growth rate of an organism to production of antibiotics and lethality analysis to name a few. FBA or, Flux Balance Analysis is the earliest COBRA method and the most widely used. But, currently, we have sub-divisions of metabolic modelling strategies which are uncovering the flaws of FBA. To fix these flaws, we have been developing multiple methods which are also being backed by experimental data. So, now we are integrating data from experiments in the models and developing methods for a much better understanding of the metabolic pathways and functionalities of the organisms. The data-driven approaches provide more information about the models and hence provide us with a deeper understanding of the networks.</p>

<p>enviroCar App is currently in fully functional state yet there are some issues which allows users to create artificial types of cars with arbitrary attributes and lead to collecting wrong data which needs to be resolved and Re implementing current database layer based on sqlbrite which has been deprecated. The project also lacks some features that will be a lot helpful to users.</p> <p>I would like to propose following idea to improve app functionality and UX with app</p> <ol> <li>Improvement of the Car Selection Process in the enviroCar Android app.</li> <li>Re implementing existing database layer currently based on sqlbrite.</li> <li>Add a walk through screen to activities for users to know about all controls in applications</li> </ol>

This project aims to enhance the search capabilities within the OpenELIS system, particularly the Search Patient module, providing users with a more efficient way of retrieving patient information. We aim to integrate a Java search engine library Hibernate Search with an Apache Lucene backend, to index key columns such as patient ID, patient name and other relevant data, providing users a faster way to search results. This will also include the integration of fuzzy search capabilities which will allow for approximate matching based on similarity, wildcard search which will allow for specified pattern matching and range search which will allow for searching for values within a specified range.

<h4>Advanced Node, Edge, Arrow Plugin Library</h4> <p>This plugin draws the desired types of nodes and arrows on a non-visible canvas. These dynamically drawn images are created in the browser as Blob type images and visualization of ccNetViz as texture.</p> <p>These pre-prepared shapes will be added to the plugin.</p> <p>The library will be able to draw the desired node and arrow graphs without compromising performance. Also, the plugin doesn't affect the core library still keep the core of library lightweight.</p> <p>With this plugin ccNetViz can:</p> <ul> <li>Basic geometric node and arrow styles</li> <li>Interactive animations for node and arrow styles<ul> <li>Color transition effect</li> <li>Shape transition effect</li> </ul> </li> <li>Custom node and arrow styles<ul> <li>Statistical node styles<ul> <li>Gauge chart</li> <li>Pie chart</li> <li>Doughnut chart</li> <li>Radial histogram, etc.</li> </ul> </li> </ul> </li> </ul> <p>With these developments, settings will be prepared and documented to enable the user to use them easily.</p>

<p>The project aims to Create and Enhance APIs and to produce a well-built backend mechanism related to an Education Platform which strives to enable 100% education and will help in upskilling developing countries and rural areas. The APIS to be created are Doubt Forum API (with Doubts and Doubt Answers), Announcements API, Mentor API, User API, CourseReview API, course Schedule API, Lecture API, and Assignments API. Each of these APIs will have proper documentation and testing. Role-based authentication along with firebase authentication had to be added to ensure that the required routes are secured along with some extra features along the way. These APIs would be used by the client-side of the app to fetch data and render quality functionality</p>

<p>Implementing an <strong>in-proxy authorization cache for envoy proxy using web assembly and proxy-WASM rust SDK</strong>. The cache will be in synchronization with 3scale Service Management API by periodically flushing the local cache snapshot and updating the local cache with a new cache snapshot provided by 3scale Service Management API. When a HTTP request is received by the proxy, it will do a look up in the cache to check whether a cache record exist for that particular request. If a record exist, then perform authorization logic based on that request <strong>(cache hit)</strong> . If a cache record does not exist<strong>(cache miss)</strong>, do a HTTP call to 3scale Service Management API to fetch relevant authorization data, add the records to the local cache for any subsequent requests and perform authorization based on the received data. For the project, <strong>a request intercepting HTTP filter</strong> and a <strong>singleton service that runs independently from request life cycle</strong> will be implemented using proxy-wasm-rust-sdk and will compile them as web assembly modules to extend envoy proxy with the HTTP filter and singleton. <strong>Web assembly modules allow us to extend envoy without building the envoy static binary using bazel build system.</strong></p>

<p>The project aims to improve and maintain at least 25 sugar activities.</p>

<h3>Problem</h3> <p>As of today, CancerDiscover has a not-so-easy build and workflow for users to conduct microarray experiments. Moreover, the current setup requires users to manually download datasets and at the same time, separately label them. Users have no visual analysis provided at any given time during the course of the experiment. Moreover, users are also limited to use the default parameters for each classifier, thus limiting a user to build more efficient prediction models. Finally, the overall workflow is poorly documented for installation and usage.</p> <h3>Solution</h3> <p><strong>candis</strong> - A minimalistic clean Graphical User Interface integrated with the current command-line tool will not only provide a smooth build and workflow for an experiment setup, but also provide <strong>remote downloading for data sets</strong>, <strong>quality control visualisations</strong> and <strong>user-defined parameters</strong> during analysis. A modular framework will also provide future extensions for more techniques. Users will also have access to a well-documented manual that eases the overall use of the proposed software. The current ongoing development of this application can be viewed at <a href="https://github.com/achillesrasquinha/candis" target="_blank">github.com/achillesrasquinha/candis</a></p>

This project will develop the core execution engine for Music Blocks 4, an educational platform that helps students explore music, mathematics, and programming through block-based coding. The Program Engine will allow users to create musical programs by arranging visual blocks and then execute these programs to generate music with precise timing. I will implement a robust Abstract Syntax Tree (AST) representation of programs, an interpreter that executes block instructions, a state manager to track variables and program state, and a scheduler for time-based musical operations. Key deliverables include a complete execution system for basic programming constructs, music generation capabilities, concurrent execution for multi-part compositions, and comprehensive error handling to provide clear feedback to users. The end result will be a performant, reliable foundation that enables Music Blocks users to create, share, and learn through interactive musical programming, with special attention to educational use cases and accessibility.