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<p>The primary aim of this project is to improve the cBioPortal’s clinical-timeline. The present implementation (<a href="https://github.com/cbioportal/clinical-timeline" target="_blank">https://github.com/cbioportal/clinical-timeline</a>) is pretty rudimentary and there is a lot that can be improved upon. There are many new features that I plan to implement so that the end users and the researchers have better tools for analyzing and visualising the data.</p> <p>Along with the features, proper unit tests will be written which will help maintain the project better, ensure it doesn’t break anytime and also demonstrate that my code works. Many unattended bugs that the timeline has will also be fixed so that it works smoothly and as expected.</p> <p>This project will provide a better toolset for clinicians to analyse the patient’s data and that in turn would help society at large. I am really passionate about this project and the fact that my work could affect the lives of millions of cancer patients across the world is highly satisfying and motivating.</p>

<p>To increase the interoperability of the Galaxy Platform with GA4GH Cloud-compliant solutions, the goal of this project is to add support for the TES to the Galaxy and Pulsar. The runner would be implemented in Galaxy, would be able to convert the job requirements from Galaxy to the job script for TES, and would stage the job on TES remotely and actively manage the sent job until its completion. This would allow Galaxy to distribute the jobs across the TES computational Network. According to the TES specification, the Pulsar REST interface could be modified to bring standardization across the services.</p>

<p>Sugar Dashboard, a user dashboard which shows user information like last activity opened, last project opened, activities installed on your device, most used activity, and visualizing them by heat maps and graphs.</p> <p>The Tamagotchi widget will replace the existing XO icon on the center of Sugar Dashboard. It will change its shape according to disk space, battery percentage etc.</p> <p>The last part is to create a journal like activity. The current Journal can not be extended/modified by the end user without making changes to core Sugar. This activity will be similar to the Journal activity, but can be modified by a user who wants to make changes. This part might also include integration of Portfolio activity which currently uses Journal objects.</p>

<p>Write a program that loads TypeScript declarations for use in the Ceylon compiler. This will allow people to use TypeScript libraries and programs, as well as JavaScript APIs with TypeScript declaration files (Browser, Node), typesafely from Ceylon (without the need for <code>dynamic</code>).</p>

OpenELIS is a critical open-source laboratory information system used globally by healthcare facilities, particularly in low-resource settings, to manage patient data, test results, and laboratory operations. As healthcare systems increasingly face cyber threats, ensuring the security and integrity of OpenELIS is paramount to protecting sensitive patient data and maintaining trust in healthcare delivery. This project aims to conduct a comprehensive security audit of OpenELIS to identify vulnerabilities, risks, and potential attack surfaces across its architecture and dependencies. The work will include threat modeling, vulnerability scanning, and risk prioritization, followed by recommendations and targeted fixes where feasible. The project will establish a strong security baseline for OpenELIS, improving trust, supporting compliance with healthcare data protection standards, and ensuring long-term maintainability for the open-source community.

<p>MusicBrainz for Android was first created in 2010-11. In the year 2019,the app went through a significant update as part of GsoC’19 .The complete codebase was shifted to adhere to the new Android Ecosystem.The relevant updates had been made.The core of the app is now clean and in a much better condition. However,basic feaures like the Tagging facility is yet to be implemented.Also,the app’s UI must be completely redesigned and implemented as it needs to have a responsive layout in order to stay relevant in the current Android Environment and to keep up to the current Android Users’ need.</p> <p>My Project is aimed at:</p> <p>1 Fixing existing design issues and integrating the android debug bridge.</p> <p>2 Completing the Tag feature in all aspects and replace the existing library.</p> <p>3 Creating and integrating a responsive UI for users for which redesigning of some existing features and adding new features are proposed.This will be done in 2 steps. In the first one, I will add backend code for them and in the second one, the necessary GUI will be added.</p>

My proposal is centered around integrating GitHub discussions seamlessly into the leaderboard repository while concurrently enhancing the scraper's type safety. This comprehensive approach will involve a meticulous refactoring of the existing Python-based scraper to TypeScript, ensuring a robust and type-safe codebase. Leveraging the power of Octokit and GraphQL, I intend to optimize the process of scraping GitHub data, enhancing efficiency and reliability. Furthermore, I aim to introduce an innovative reward system for contributors, incentivizing active participation and fostering a collaborative environment. This system will recognize and reward contributors when their discussions are marked as answered, along with receiving an empathy badge as an acknowledgment of their valuable contribution. Overall, this proposal represents a strategic amalgamation of technical refinement and community enrichment, aligning with the overarching objectives of the project while enhancing its functionality and user experience.

<p>Reference sequences are files that are used as a reference to describe variants that are present in analyzed sequences and play a central role in defining a baseline of knowledge against which our understanding of biological systems, phenotypes and variation are based upon. Reference sequence files often use different naming schemes to refer to the same sequence and thus there is a strong need to be able to cross reference chromosomes/contigs using different nomenclatures. My project focuses on creating a centralized database and an alias resolution service that can cross reference accessions easily and reliably. A web service that allows users to access these services from any client is also required. It need to have a mechanism for manually or periodically ingesting new aliases from a remote data-source.</p>

<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. There are many activities which have not been maintained or updated for over a decade. It is important to port such activities from python 2 to python 3 along with porting them to Gtk+3. The support for python 2 is being withdrawn and the port to Gtk +3 to have a fully functional activity is important. Inaddition to that, the activity might require porting</p> <ul> <li>from GObject to GLib</li> <li>from GConf to Gio.settings</li> <li>from GStreamer Gst.Message.structure to get_structure()</li> <li>and porting to TelepathyGLib</li> </ul> <p>My project also includes adding feature improvements or fixing the features of the activity which are not working and fix display resolution issues. I will be collaborating with others to prepare activities for release and also test debian packages if needed. It is important to identify if the tracebacks are due to activity code, changes in versions of packages or due to difference in the test environment.</p> <p>So this project aims at making necessary changes to sugar activities to have at least 25 release ready activities.</p>

This proposal defies the roadmap that i am going to follow for adding search&query, REST API, duplicates and reactive API support as well as implementing a Quarkus extension of Infinispan. I created some sub-tasks with estimation of hours for each to give clearer guidance.

<p>MusicBrainz has recently been plagued by spam entries, most of them attempting to advertise other websites. SpamBrainz is the latest *Brainz project, designed to provide a future-proof, self-learning solution for combating spam that can also be adapted to work for other MetaBrainz projects.</p>

Modern AI systems relying on Retrieval-Augmented Generation (RAG) often suffer from stale data due to batch-based updates. This project, PyDebeziumAI, aims to solve this by enabling real-time synchronization between databases and LLM pipelines using Debezium Change Data Capture (CDC). The project will extend pydbzengine to stream CDC events directly into LangChain and LangGraph by transforming database changes into semantic Document objects and updating vector stores in real time. Key deliverables include: - A Python library integrating Debezium with LangChain/LangGraph - Real-time vector store synchronization (Chroma, PGVector, Milvus) - Pluggable document transformation and ID strategies - End-to-end examples (RAG chatbot, reactive agent, dashboard) - Full documentation, testing, and PyPI release This will provide a production-ready bridge between CDC systems and AI frameworks, ensuring always up-to-date LLM context.

<p>Candis (portmanteau of Cancer and Discover) is an Open Source data mining suite (released under the GNU General Public License v3) for DNA microarrays that consists of a wide collection of tools, right from Data Extraction to Model Deployment. It has a RIA( Rich Internet application) and a CLI (command line interface) to carry out research. My main focus will be on enhancing RIA part of the project.</p>

<h4>Platform Independent enviroCar App</h4> <p>enviroCar is a Citizen Science tool that is used by citizens, traffic planners, scientists and companies to collect and analyze vehicle information in various traffic situations and gain insight to support the development of sustainable traffic concepts.</p> <p>The enviroCar Android App connects with a car's onboard sensors via OBD-II and records the sensors data to generate real-time information like vehicle speed, revolutions per minute and calculates additional information, such as fuel consumption, estimated fuel cost and CO2 emissions. The only limitation being that it is only available for Android users.</p> <p>This summer I will be working closely with the community and mentors of 52°North to lay the foundation of a platform independent enviroCar app to allow iOS users to access the amazing features of enviroCar.</p>

<p>The project aims to create a platform for hosting and sharing Vega and Vega-Lite visualizations. It will facilitate a user to save, fork and publish any visualization on the web. It is designed keeping in mind the user-benefits and covers everything from back-end to front-end with few new features. It will be integrated into the editor itself so that the user can conveniently make and share the visualization from the same place. This lowers the barrier to entry into the vega ecosystem.</p>

Milvus currently lacks a Debezium source connector, meaning data can flow into Milvus (via sink connectors) but not out of it into the broader data ecosystem. This critical gap forces users into manual workarounds for data replication, auditing, and prevents the creation of hybrid pipelines that join vector search results with relational data. The plan is to implement a Hybrid strategy focused exclusively on the future-proof Milvus 2.6+ StreamingNode architecture. This approach will leverage two separate sources to guarantee a complete and ordered change stream: Woodpecker Streaming Service (WAL): Used as the only source for all Data Manipulation Language (DML) events (inserts and deletes). Etcd Watch: Used as the cleanest source for all Data Definition Language (DDL) events (schema changes), which simplifies parsing and aligns with Debezium's schema history mechanism.

<p>The purpose of this project is to implement some of that missing features as well as functionality that will be unique to the iOS client. Various advanced features will be implemented like CallKit, 3D Touch, Onboarding tooltips, etc.</p>

<h3>Description</h3> <p>InterMine is an open source data warehouse which is used to store complex biological data. It is currently using PostgreSQL as the database. This project aims to develop a prototype of InterMine which is based on Neo4j, a graph database.</p> <h3>Goals</h3> <ul> <li>Adapt the existing XML model to represent the nodes, relationships and their properties in Neo4j.</li> <li>Develop a module for generating a schema as per the existing data in Neo4j and store it in the database itself. Also, expose an API to query the schema/metadata.</li> <li>Develop a module which can take Path Query XML as input and can generate equivalent Cypher which can be queried against the InterMine Neo4j graph.</li> <li>Develop a RESTful API based on JAX RS to expose the query service. Document the API using Swagger.</li> </ul>

<p>cBioPortal allows the analysis and visualization of published cancer genomic datasets. These datasets must be queried by entering symbols of genes of interest. "OQL" keywords can also be added to further refine the query.</p> <p>My project focuses on improving the querying experience on cBioPortal. This is done by giving users visual feedback regarding the correctness of the symbols that they have entered. For incorrect symbols, similarly-spelled valid symbols are provided as suggestions. This is useful when a user has misspelled a gene symbol, or has entered an incomplete/ambiguous symbol. Furthermore, when a user wants to enter OQL keywords, a multi-level prompt menu is provided where a user can choose keywords and see a description of what they mean. Upon selecting it, the keyword is added to their query.</p>

<p>vcf2fhir is a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. The utility currently converts simple variants (SNVs, MNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA. This project aims to enhance the utility by adding capabilities for the conversion of structural variants (e.g. insertions, deletions, copy number variants).</p>

<p>The aim of this project is to build a compliance framework, to ensure that all new implementations/products/APIs adhere to the central specification defined by GA4GH. This framework would consist of pre-defined tests which can be reused for testing any new products for compliance during the product approval process, thereby reducing the cost of writing tests again and again. The framework would also include meaningful logging and a final report generation. The final reports would be published on a public website.</p>

<p>UCSC Xena is a functional genomics visualization and analysis platform. For this (genomics visualization and analysis), there are many datasets which are provided by data hubs available with Xenabrowser itself which users can use. The data hubs are: UCSC Public Hub, TCGA Hub, Pan-Cancer Atlas Hub, ICGC Hub, UCSC Toil RNAseq Recompute, Treehouse Hub and GDC Hub. Our discussion of interest lies in GDC Hub.</p> <p>GDC (Genomic Data Commons) Hub fetches data from the GDC repository: <a href="https://portal.gdc.cancer.gov/repository" target="_blank">https://portal.gdc.cancer.gov/repository</a> via the GDC API. However, the data on the Xena is not updated. Current Xena data was updated on release 10, roughly 1.5 yrs ago. This project mainly revolves around updating data on xena with the current release (release 15). This will also simplify the process of adding data to Xena removing the XML files as a source.</p>

Enhance the translation interface in MediaWiki to offer real-time translation previews and structured translation statistics.