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<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>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 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>

The aim of this project is to make it easier to use MaveDB datasets for clinical use, as most of the MaveDB datasets are not annotated in a way that allows them to be combined with other genomic data. Datasets in MaveDB will be mapped to the human genome using the GA4GH Variant Representation Specification (VRS). This can be achieved by mapping sequences using alignment algorithms, transforming the results into VRS objects, and validating the results.

<p><a href="https://github.com/xiph/rav1e" target="_blank">Rav1e</a> is an AV1 encoder that is fast enough to be used in videoconference scenarios on x86_64. This project will implement <a href="https://github.com/WebAssembly/simd" target="_blank">wasm-simd</a> support in rav1e to make viable as in-browser encoder.</p>

<p>WebDriver is a remote control interface that enables introspection and control of user agents. Currently, Servo supports only a minimal subset of the WebDriver protocol. The goal of this project is to extend this support and pass the conformance tests to demonstrate the implementation's correctness. Additionally, the project also aims to support running WebDriver-based automated tests like the WebBluetooth test suite, which require complex browser control and automated interactions that WebDriver provides.</p>

<p>The end goal of this project is to make the entire Sugar Code compatible with both the major versions of Python.</p> <h5>Importance:</h5> <p>The project is critical since libraries like GStreamer are drawing their support from Python 2 and support for Python 2 is also about to end.</p> <h5>Description:</h5> <p>The project involves the following milestones:</p> <ul> <li>Port the static bindings of Telepathy to their PyGI counterpart</li> <li>Port the automake files to install the toolkit for both Python 2 and Python 3</li> <li>Port the C extensions of Python to be compatible with Python 3</li> <li>Port the Sugar toolkit to make it Python 2 and Python 3 compatible</li> <li>Port the Sugar OS and Activities to Python 3</li> <li>Release the corresponding new versions and Debian and Fedora Packages</li> <li>Rewrite the entire documentation</li> </ul>

<p>Making information easily accessible to people, when and where they need it. Part of a greater effort to make Sugar more welcoming and maintainable.</p> <p>Script for end-to-end migration of <a href="https://wiki.sugarlabs.org/go/Activities#Sugar_Activities" target="_blank">activity documentation pages</a> from the Sugar Labs wiki, to GitHub(and simultaneously <a href="https://github.com/godiard/help-activity" target="_blank">help-activity</a>).</p> <h7>Impact:</h7> <ul> <li>Reduction in maintenance efforts.</li> <li>User-documentation moved to help-activity could just be downloaded once, and then read whenever needed; eliminating the need to have persistent internet connectivity.</li> <li>Contextual-help ( <code>alt</code> + <code>shift</code> + <code>h</code> ) from within another sugar-activity could also be made available, when the documentation resides at help-activity.</li> <li>Developer-documentation of sugar-activities, if kept at same place with the source-code in its GitHub-repository; would help developers/maintainers (they could be read and updated easily; without visiting an external link to the wiki).</li> </ul>

<p>TaskCluster workers are hosted on services such as EC2 and currently expose ports to the internet to allow http-clients to call API endpoints. This setup may not be feasible in a data center setup. Livelog proxy aims to mitigate this problem by allowing workers to connect to the proxy over an outgoing websocket connection and exposing API endpoints to the internet. Any incoming requests will be reverse proxied to the worker over its outgoing connection. This is implemented as a distributed system to handle high amounts of traffic.</p>

<p><strong>Hibernate Search</strong> is an extension to Hibernate ORM that brings the powers of full-text search via <a href="https://lucene.apache.org" target="_blank">Lucene</a> and <a href="https://www.elastic.co" target="_blank">Elasticsearch</a> to JPA models. Think of it as Google: after processing the input keywords (e.g. ignoring stop words and applying different kinds of normalization), Hibernate Search returns results ordered by relevance. It brings significant benefits comparing to normal SQL for search-related uses cases. Its full-text index can be updated in two ways: Automatically, whenever data changes (using listeners hooked into Hibernate) or by means of the "mass indexe", which rebuilds the entire index for given entity types.</p> <p><strong>This proposal aims to provide an alternative to the current mass indexer</strong>, based on the Java Batch architecture as defined by <a href="https://jcp.org/en/jsr/detail?id=352" target="_blank">JSR 352</a>. This standardized tool <a href="https://jcp.org/en/jsr/detail?id=352" target="_blank">JSR 352</a> provides task-and-chunk oriented processing, parallel execution and many other optimization features. This batch job should accept the entity type(s) to re-index as an input, load the relevant entities from the database and rebuild the full-text index from these.</p>

<p>The overall goal is to make it possible for editors of themes to feel comfortable working directly with the theme editor. Allowing users to search for text within files and name of files, easily upload and move files with the HTML 5 grab and drop feature, and improve the user interface are the main goals for this project.</p>

<h3>Goal</h3> <p>This project aims at fully implementing end-to-end encryption in matrix-python-sdk, following the official implementation guide and making use of the Python bindings already present in libolm.</p> <h4>Rationale</h4> <p>Currently, even though end-to-end encryption has landed in Matrix for over a year, only the three SDK upon which is built Riot on different platforms (JS, Android and iOS) ship with encryption. On desktop, this situation prevents writing clients, bots and bridges that can interact with encrypted rooms in any other language than javascript. Tackling this issue would benefit the matrix ecosystem by seeing more featureful projects emerge in a variety of languages (Python in this case). It also supports the Matrix long-term goal of having E2E encryption turned on by default in private rooms.</p>

<p>We all know that nowadays a website needs a responsive layout, by the fact that there are a lot of different devices sizes, like smartphones, tablets and desktops. In addition to this, the project organization is another important thing: letting the code more readable and easier to maintain helps the developer to modify the code when something goes wrong. Another important thing that we can't ignore is the website performance, this one depends of the website weight, but, why performance is important? Because nowadays people wants instant information, since they have a hurry life. This project has as main goal to give these three important things to the OpenSNP website.</p>

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.

<p>This project aims to add a right sidebar to the minimal Hydrogen matrix client that shows :</p> <ul> <li>Room Information</li> <li>Memberlist</li> <li>Member Information </li> </ul> <p>In addition, this project also aims to implement SSO login.</p> <p><a href="https://matrix-org.github.io/gsoc/#/projects?project=hydrogen&amp;lang=en" target="_blank">Link to Matrix gsoc page</a></p>

Genomic data sharing is slowed by manually cross-checking consent and data-use language against dense GA4GH and related policy text, while generic LLMs risk hallucinated citations. This project extends GA4GH-RegBot, an open-source RAG assistant that ingests policy PDFs into a Chroma vector store with a BM25 manifest, retrieves with dense embeddings plus BM25 fused via reciprocal rank fusion, and generates structured compliance JSON with hard grounding: chunk-ID allow-list verification with automatic retries and token-overlap filtering on the LLM path. Deliverables across the GSoC period include hierarchy-aware parsing and richer metadata for GA4GH PDFs, cross-encoder re-ranking on top of the existing hybrid stack, an open-source LLM path alongside the current OpenAI integration, Streamlit and CLI updates, Ragas or TruLens-based evaluation with documented thresholds, expanded tests and CI, and polished documentation for contributors and REWS stakeholders.

OncoKB™ is a crucial resource which provides comprehensive information about genomic alterations in cancer. However, despite the availability of APIs and annotation tools, some users, especially those without computational backgrounds, face challenges in effectively annotating variants and generating reports. To bridge this gap, my project seeks to publish a standalone npm package for visualization of OncoKB annotations and a report generation module to make the annotations downloadable by the users. Seamless integration of these modules with cBioPortal will mark the end of my project.

The Task Execution Service (TES) API and the Workflow Execution Service (WES) are two of the several standards defined by the Global Alliance for Genomics and Health (GA4GH). The global picture is that TES and WES are designed to complement each other in running workflows by first identifying and scheduling the different individual tasks in the right order (WES) and then executing them in a containerized manner. This project is the implementation of a federated mechanism of task execution, i.e., different tasks of the same workflow will be executed in different Kubernetes clusters. These clusters can be in different geographical locations and be managed by different institutions. This can be achieved by introducing a dedicated “gateway TES” implementation, which receives an incoming task, runs a task distribution logic middleware to identify, out of several options, the most suitable TES instance, then relays the incoming task to that instance.

<p>In mass spectrometry the isotope pattern of an unknown molecule consists a powerful analytical tool to identify its molecular formula. Modern technological advancements led to a resolution increase in mass spectrometers. This enables mass spectrometers to distinguish parts of a molecule's isotopic fine structure.</p> <p>To determine whether a presumed molecular formula is observed within a mass spectrum the theoretical isotope pattern of the formula needs to be calculated.</p> <h3>OpenMS implements only one theoretical isotope pattern generator that calculates a low resolution version of the isotopic structure. The additional information that a mass spectrometer provides may be absent in a low resolution theoretical isotope pattern and potentially restricts scientists of excluding possible identities of a certain molecule.</h3> <h3>This proposal aims to enrich the OpenMS isotope distribution class with the implementation of three new algorithms for calculating high-resolution isotope patterns.</h3> <p>Ιt proposes an algorithm that belongs in the class of polynomial multiplication methods and two algorithms that consist variations of the Fourier transform methods.</p>

<h3>Adaptive Quantization based on an activity mask.</h3> <p>The human eye is more tolerant towards errors in areas of high activity and is quick to find out errors in areas of lower activity. To leverage this psychovisual characteristic, quantization can be made adaptive based on the activity mask. Activity masking will be implemented in two phases:</p> <ol> <li>Biasing the RDO based on the activity at a specific region.</li> <li>Varying the quantizer offsets across segments based on activity.</li> </ol> <h3>Optimizing the quantization algorithm using Trellis Quantization:</h3> <p>Using Trellis Quantization passing the activity measurements as the weights to the trellis. The output of this Activity masked Trellis is used for quantization. This helps the quantization perform better in PSNR metrics while increasing perceptual image quality significantly. This is a feature that has proved to perform better in the case of x264 and is expected to yield similar results at rav1e too.</p>

<p>In order to visualize their private datasets, users of UCSC Xena browser have to upload data using separate desktop application. This behavior does not fit preferred workflow, since all visualizations are carried out in the browser and using desktop client only for uploading data is confusing for some users.</p> <p>The goal of this project is to move existing data upload functionality from desktop client to the browser. In addition to that, import module would be improved with extensive error handling and uniformed user experience overall.</p>

<p>Currently Listenbrainz uses MSIDs (Messybrainz-ID) for retrieving useful user stats (e.g. <a href="https://beta.listenbrainz.org/user/iliekcomputers/artists" target="_blank">user listens</a>). Now ListenBrainz also plans to generate data which could be used by MusicBrainz to show useful information like artist popularity. MusicBrainz has MBIDs (MusicBrainz-ID) associated with each artist, recording, and release. In order to provide MusicBrainz with the ability to access information based on MBIDs, we have to associate recording_mbids, artist_mbids and release_mbids to the listens where we can. For most of the listens we don’t have artist_mbids and relesae_mbids associated with them. But have recording_mbids associated with them. So, now I plan to associate MBIDs to MSIDs.</p>

The objective of this proposal is to implement a new data fetch layer for frontend in Plone CMS. I intend to implement a library “@plone/client” that will work as a client for “plone.restapi”, using Tanstack Query. This client will enable Plone to move away from the “AsyncConnect” data fetch layer that is based on Redux. Then Redux can be used as the application-level data store only. TanStack Query brings many benefits with it, like caching support, de-duplication of queries, cancellation, refetch, easy-to-use hooks, SSR support, and more. A modern API client should use these features fully. The primary goal of this client is to be robust, yet flexible enough to support all use cases, and be easily extensible.