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<p>TreeMatcher is a subproject of ETE3. Target of TreeMatcher is to perform search on phylogenetic trees using tree patterns that allows relax connection between tree nodes in newick format mimicking regular expressions' functionality.</p>

<p>I would like to work on issue #70, “OncoKB Analysis in Study View”. An inconvenience for both biologists trying to get valuable information to make informed decisions on prognosis and patients who would like to readily have access to this information for their own comfort, is the time needed to access this data. As the genomic data sets for each study vary in size, viewing annotations for studies that have large data sets in real-time is a challenge because it takes a while for the information to load. For example: MSK-IMPACT 2017 has a data set of 10,000 samples, so it will take a few minutes for the study view to load. I would like to work on the three backend tasks and first frontend task. This means pre-annotating the mutation data and storing it into the MySQL database and creating an additional column in the mutation table called “annotation”. Querying and using the web API to provide the information needed to solve the front-end goal of creating pie charts for oncogenicity and highest level of sensitive therapeutic implications per sample.</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>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>

The goal of this proposal is to address the issue of how difficult it can be to package and reuse computational workflows and analyses in genomics and health research since diverse data and workflow standards don't always work together seamlessly. By creating a Python library and related command-line tool that enable bidirectional conversion between RO-Crates (with pertinent computational workload profiles) and GA4GH WES/TES payloads, the RO-GA4GH Bridge project seeks to address this issue.

<p>This project aims to provide dynamic lighting and shadows in GDevelop using PixiJS. Plugins such as Pixi-layers, Pixi-lights and Pixi-shadows would be integrated with the game engine to achieve this.</p>

<p>This project aims to improve the current active sampling strategy by implementing other information measures such as information density and diversity based on the embeddings produced by known open deep learning models that uses either supervised or unsupervised approach</p>

<p>Genpipes is a set of software pipelines designed for genomic analysis. There are currently seven different pipelines and three more are in the development phase. These pipelines consist of several steps (10-40). Therefore keeping track of which step was executed, what functionality did it provide, at what time it was executed, whether it failed or succeeded can be a cumbersome task. The project consists of an integrated system that automatically builds a flowchart of the steps executed by the user. This would be a user-friendly add-on to the software as having a flowchart of the steps executed would help in the analysis and understanding of the process performed.</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>

<h4>Jérémie Amsellem</h4> <p>Full proposal is available at : <a href="https://wiki.sugarlabs.org/index.php?title=Summer_of_Code/2016/SugarizerOS" target="_blank">https://wiki.sugarlabs.org/index.php?title=Summer_of_Code/2016/SugarizerOS</a></p>

<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>

This project aims to modernize the Speak Activity by integrating a large language model (LLM) & small language model (SLM) to enhance the chatbot and integrate a modern TTS model to improve the voice features, making it more educational and engaging for early learners. The Speak Activity, traditionally used for promoting reading skills through synthetic speech, will be upgraded to provide a more natural and interactive experience. The primary objective is to implement an LLM-based chatbot offering improved conversational abilities and a more human-like interaction style. For the voice feature a high-quality, natural-sounding Text-to-Speech (TTS) model that accurately handles pronunciation and phonetics will be used. By fine-tuning the LLM to manage invented spelling and grammatical inaccuracies, the chatbot will offer a supportive and child-friendly interaction, guiding learners in an encouraging manner. The project will utilize Python and a fine-tuned model hosted on the cloud and accessed via an API endpoint. This design ensures compatibility and seamless integration with the existing Speak Activity, without adding extra dependencies. To support offline functionality, a lightweight, fine-tuned fallback model will be packaged with the activity. This fallback ensures continued usability even without an internet connection, albeit with slightly less accurate responses compared to the cloud-hosted model. This enhancement will make the Speak Activity a more effective and child-friendly tool, promoting better language learning through engaging and conversational interactions.

<p>With the development of software container technology, developers can manage and deploy their software effectively. The software can start up and run on the container more and more quickly. The Dockstore is a platform for users to share tools encapsulated in Docker. Furthermore, in order to share tools as seamlessly as possible, GA4GH create a set of APIs for the biology scientists. In this project, I would like to make the Dockstore support these APIs. In this way, people can create their tools based on the APIs so that their tools can be work with others’ tools seamlessly. It will absolutely help the cooperation between scientists due to they can create their tools based on or cooperate with others’ more easily. Our project has three main goals. The first is to communicate with GA4GH community so as to decide the APIs standard and their implementations. Then, I need to implement and test these APIs with java so that the Dockstore can support the APIs. The last goal is realize cross indexing of tools across all sites that support the standard. When finish cross indexing, Dockstore can search all the tools from all websites which support the standard.</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>

<p>The current representation of reference genomes is as a sequence of nucleotides akin to a long string. Intuitively, this doesn’t represent a genome but rather a consensus. A workaround used today is holding variation data in VCF files that don’t update the reference meaning the reference will always represent the genome as it <strong>was</strong> not as it <strong>is</strong> or as it’s <strong>evolving</strong>. It’s clear that the current method of representing genomes is not ideal. There is a need for a representing the reference in a data structure that contains its inherent variation. Different methods have been tried and the variant graph is a promising one. The way the graph works is by representing the variation within the genome as alternative paths one can traverse the graph through and conserved regions as nodes without alternative paths to the get to the next node; we then index the nodes for querying and alignment. Moreover, variation graphs hold an advantage with rapidly evolving genomes and short read data that could get thrown out when it doesn’t have a place to align to in the reference; with the variant graph short reads should reads could align to alternative nodes.</p>

Concerto, the core modeling language of the ACCORD PROJECT, is critical for smart legal contracts and domain modeling. This project aims to migrate from the current testing framework mocha to vitest which will enhance the performance, execution time and debugging capabilities. This process can be automated by the combination of vitest-codemod, regex transformations, ai assistance and some manual scripts required for handling complex test cases which cannot be automated. Here are the deliverables: 1. Migration from Mocha, Chai, Sinon to Vitest for all Concerto implementation. 2. A new Concerto conformance package which will be a standalone validation test package for all Concerto implementations.

<p>Sugar Labs has more than 250 activities GitHub and elsewhere which have scope for improvement. Since the support for Python2 was withdrawn from Python Foundation, porting the activities to Python3 and GTK+ 3 is very crucial. My work on this project includes,</p> <ul> <li>Porting activities to <strong>GTK+ 3</strong> and <strong>Python3</strong>.</li> <li>Implementing <strong>basic game design features</strong> which attracts the children (activities from <em>Honey</em>).</li> <li>Implementing <strong>original design features</strong> (activities from <em>Fructose</em> ).</li> <li>Adding <strong>activity specific features</strong> to enhance <em>User Interface</em> and <em>User Experience</em> .</li> <li><strong>Testing and modifying</strong> the activities to ensure at least <em>15 activities are read to release</em>.</li> </ul>

<p>My proposed project is inclusion of Timbre Widget to Music Blocks. Timbre is a character of a sound that distinguishes it from other sounds. With the addition of the timbre widget, users of Music Blocks can tweak timbre of a sound and have a real-time view of the parameters they are applying to a particular sound. The users can apply effects , change the attack,decay ,sustain and release(ADSR) envelope of the sound and can apply filters to the sound.When the users change the timbre of the sound, they can also visualise how the timbre is being actually changed with the help of pictorial representation such as graphs.</p>

<p>The project aims to create a platform for hosting and sharing Vega and Vega-Lite visualizations as well as integrating the share functionality with the current editor. It will facilitate a user to save, fork and share any visualization on the web. It is designed keeping in mind about user-benefits and covers everything from backend to frontend with few new features. It will be a specialized platform for declarative Vega and Vega-Lite visualizations that lowers the barrier to entry into the ecosystem. Hence improving the ecosystem.</p>

<p>Rust's procedural macros can be one of the more complicated and difficult to read sections of any codebase. A well-implemented and easy to use macro greatly improves a codebase by removing boilerplate code and user-facing complexity. My goal for the internship is to make the <code>ruma</code> macro crates readable and easy for newcomers to follow and add to. This will allow easier debugging and enable more people to review pull requests in the code-gen heavy crates. I plan to implement macro testing using <a href="https://github.com/dtolnay/trybuild" target="_blank">trybuild</a> or <a href="https://github.com/eupn/macrotest" target="_blank">macrotest</a> for both <code>ruma-events</code> and <code>ruma-api</code>. I will improve the error messages of the <code>proc_macro</code>s in <code>ruma-api</code> and <code>ruma-events</code> by using relevant spans and crafting helpful suggestions or examples to emit to the compiler, so the user knows exactly where and how to fix their code.</p> <p>The other goal of the project is to implement new code generation macros for the next breaking release version of <code>ruma-events</code>. The release will contain a major rewrite of how the event types are structured themselves and within collections. I will work on generating code for the new collection types and adapt existing code generation to the new API.</p>

The Music Listening History Dataset is pretty damn impressive; It contains ~27 billion logs of real-world data from last.fm scrobbles distributed into 18 chunks summing up to ~611.39 GB of compressed text files. This results in 583k users, 555k unique artists, 900k albums, and 7M tracks. Here each scrobble is represented in the following format: timestamp, artist-MBID, release-MBID, recording-MBID. (Source: https://simssa.ca/assets/files/gabriel-MLHD-ismir2017.pdf) Unfortunately, this data has some significant fallbacks due to last.fm’s out-of-date matching algorithms with the MusicBrainz DB, resulting in frequent mismatches & errors in the recording-MBID data, affecting the quality of the available dataset. Overall, the goal of this project is to create an updated version of the MLHD in the same format as the original, but with incorrect data resolved and invalid data removed.

<p><a href="https://github.com/deislabs/smi-metrics" target="_blank">SMI-Metrics</a> aims to have a commen interface to get metrics from servish mesh implementations. Applications, Tools can be built targeting this interface without having to write anything specific to an implementation. Users also don't have to learn the APIs of each mesh but rather have this shim in their kubernetes cluster which provides a common API. As the <a href="https://github.com/deislabs/smi-metrics" target="_blank">smi-metrics</a> repo is pretty new, my work is to take care of this whole repository i.e CI, bugs, etc while also implementing the support for Istio and Consul Connect Service Meshes.</p>

Currently, running picard always spawns a new instance. It would be useful to pass the arguments to an already running instance (if exists). The best way to achieve this is to utilize named pipes, they work on all supported operating systems (i.e. Windows, Linux, MacOS). This project is part of the big Picard 3.0 update. To learn more, read: https://github.com/skelly37/GSoC-2022