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<p>The VCF (Variant Call Format) is a format for text files, which is generally stored in a compressed manner to make the data retrieval of variants fast. The data which is redundant is not stored, only the variations are stored. VCF files are used to store all variant types which includes single nucleotide polymorphism (SNP) in a specific position of the genome, short insertions and deletions (INDEL) and structural variants (SV). VCF-validator includes various checks to ensure that the VCF file is consistent. It is based on a formal grammar and performs lexical, syntactic, and semantic analysis of the VCF file. It also includes a tool called VCF-debugulator which fixes errors such as the presence of duplicate variants automatically. SNPs and INDELs are fully supported in VCF-validator, but the support for SVs is still limited. The aim of this project is to improve the support for structural variants in the validator and the debugulator.</p>

<p>The Global Alliance for Genomics and Health aims to provide end-to-end solutions for clinical data use cases. The sensitive nature of data in the personalized healthcare sector frequently requires it's analysis on-site. Computation over the cloud allows the user to enjoy flexibility in hosting the data and its computation. Through this project, I aim to provide a proof of concept for a microservice that redistributes Task Execution Schema instances generated from the Workflow Execution Schema engine(s) based on parameters associated with data or the workflow ex. the time required to transfer data cost associated with the computation of the task etc.</p>

<p>This project aims to extend Graphback by adding additional capabilities by building custom plugins. Plugins will provide Data Synchronization and Conflict resolution by optional integration with Debezium. Additionally, this project also aims to prototype an example application using the Graphback runtime with Debezium integration and deploy it using Knative.</p>

The CARE project aims to enhance healthcare management by digitizing patient records, streamlining workflows, and enabling TeleICU services.My proposal aims to improve the efficiency and streamline the PDF report generation process within the CARE system. The current browser-based rendering approach can be resource-intensive. I plan to implement Typst to generate PDF reports. This solution promises to reduce resource overhead and potentially improve performance. My project will involve evaluating Typst's capabilities, adjusting templates, benchmarking resource usage, and gathering user feedback to ensure a smooth transition. My goal is to enhance the report generation workflow, ultimately benefiting the CARE system.

<p>The majority of contemporary genomics and transcriptomics research is carried out using short-read technology such as the output of Illumina sequencers. However, newer long-read technologies such as PacBio and Oxford Nanopore (ONT) are becoming more prevalent due to the advantages they offer over short reads. The main advantage of long reads is that they span a much larger portion of the genome or transcriptome, making it easier to detect events such as structural variants or isoforms. As more researchers begin to take advantage of long reads, GenPipes needs to evolve and support long-read technology in its main pipelines. The objective of this project is to create a new RNA-seq pipeline (rnaseq_longreads), that supports long-read inputs. The new pipeline will be created based on the current versions of the RNA-seq pipeline, with the addition of the minimap2 aligner as well as StringTie v2 and Ballgown for generating transcript counts. In addition to implementing a long-read RNA-seq pipeline within the GenPipes framework, short-read RNA-seq pipeline will also be updated to utilize StringTie2 and both pipelines will be tested to ensure that they are working properly.</p>

<p>This project aims at making Sugar run perfectly on the Raspberry Pi like it does on the XO laptops and to create an image of Sugar which is suitable for inclusion on the Raspberry Pi organization's download page.</p> <p>Goals of the project:</p> <ol> <li><p>Make a Raspbian image of the Sugar desktop environment which can be flashed on the SD card of the Raspberry Pi. An “image” in this case is an array of data blocks for a micro SD card which will contain a partition table, a boot and root filesystem specifically designed for the Raspberry Pi.</p> </li> <li><p>Document the whole process and publish a script showing how others can make the image themselves.</p> </li> <li><p>Ensure all the activities work well or are removed from the image.</p> </li> <li><p>List the Raspbian Sugar desktop image on Raspberry Pi Foundation's downloads page.</p> </li> </ol>

<p>This proposal is focused in network visualization layouts. I intend to implement canonical algorithms for ccNetViz and to develop variations. Most significantly, I think that the Hive layout might be enhanced by enforcing undulations on the lines. I plan to properly document the layouts with examples and well commented code.</p>

<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>MusicBlocks is going through a complete overhaul to MusicBlocksv4 , allowing us to work on a new, improved version with the latest tech stacks and enhanced performance. The Toolbar in MusicBlocksv3 needed a refactor in terms of both design and internal implementation. Music Blocks also requires a new system design and a better, more suitable architecture to support the working of the platform. The functionalities in the toolbar needed to be better organized in a way that would enhance the User Experience and provide the most suitable accessibility to them. This project aims to build a better, more maintainable Menu Framework along with connections with the Canvas ArtBoard and consisting of numerous features segregated into suitable categories.</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>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>

<p>The streams based workflow engine will organize tasks into streams, allow parallelization of this streams, and work locally as well as integrated into common external HPC services. As well dat can be integrated to store intermediate and final data. This provides a framework for efficient, reproducible, and understandable bioinformatics pipelines.</p>

<p>Currently CritiqueBrainz’ users can review release groups, events, and places. This will be expanded on by implementing reviews for other MusicBrainz entities (works, artists, recordings, labels). This metadata will be retrieved from MusicBrainz through the mbdata module, and the CritiqueBrainz back-end and the front-end will be extended to support reviews for these entities.</p>

<p><a href="https://knative.dev/" target="_blank">Knative</a> is an open-source community project that extends Kubernetes with modules for deploying, operating, and maintaining serverless, cloud-native applications. The serverless cloud computing model has the potential to improve developer efficiency while decreasing operating costs.The project idea is to develop Charmil, an open-source Golang-based platform that will serve as a package manager which assists in the discovery and installation of plugins from a community-curated plugin index. These plugins can then be embedded into any host CLI with additional features such as new version detection and smooth upgrades.Through Charmil, each CLI will be able to install other CLIs as extensions, thereby organizing them in a hierarchy. This functionality of Charmil will later be used to add new features on top of the Knative CLI.</p>

<p>My project is to implement a complete micro blogging system on top of Matrix. With the available infrastructure, I can build a web client for Matrix designed specifically for this.</p>

Develop distributed edge caching strategies using Web Standard Cache API for sub-50ms storefront responses.

<p>This project aims to continue on the development of the Musicbrainz Android App further, complete the Tagger implementation, introduce ListenBrainz and CritiqueBrainz functionalities to the app, revamp the UI for a more user-friendly experience, work on documenting the Code, Design, GitHub repository, and all the implementations in the best manner possible while moving the codebase to Kotlin completely.</p>

<p>Through this project I plan to improve the genome overview in the patient view page. By adding- 1) Zoom Feature 2) Introducing Probe Level Copy Number Data 3) Filtering feature (Showing the overview for only a subset of samples)</p>

This project extends the Accord Project Template Playground by implementing an end-to-end, sandboxed logic execution pipeline to solve its inability to test interactive smart contract behaviors natively. By utilizing a secure Web Worker architecture, the platform will safely evaluate user-authored TypeScript logic and validate all states and requests against strict Concerto models directly in the browser. The core deliverables include an integrated Monaco-powered logic editor, an interactive contract runner UI for initialization and request handling, dynamic execution results visualization, and comprehensive multi-state contract templates. Together, these features transform the platform from a static authoring tool into a complete, interactive development workspace for smart legal contracts.

<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>

<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>

<p>Bookbrainz lacks a feature which allows a person to make a collection of entities (edition, edition-group, work, author, publisher) for his/her future reference. This project is about introducing such a feature - User Collections.</p>

The current logging system for Matrix communications at MeB relies on an unmaintained IRC-based bot (BrainzBot) that logs messages to a PostgreSQL database and displays them on chatlogs.metabrainz.org. While this system works, it uses outdated technology with known vulnerabilities, doesn't support many of Matrix's features and is no longer suitable as Metabrainz' primary communication platform. This project proposal replaces BrainzBot with a new archival service that archives messages directly from Matrix to HTML files and a PostgreSQL database. It will support Matrix features like message editing, reactions and media, and provide full text search over all messages. Both historical and new messages as they come in will be archived.