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<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 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>

Crypt4GH is a file format developed by GA4GH that keeps genomic data encrypted at rest and in transit. Currently, implementations of the TES API do not support processing Crypt4GH files. I propose an implementation of the TES API that handles Crypt4GH files through the use of middleware that alters the initial TES request in order decrypt Crypt4GH files before processing. First, I will create a "TES playground" that is able to run a simple task. Then, I will add to the functionality of this playground in order to demonstrate an implementation of the TES API that can handle a Crypt4GH-encrypted file as an input. This project will hopefully serve as a proof-of-concept to inform future standard-setting works.

Open-source developer portfolio and event hub for connecting open-source contributors and mentors.

<p>The primary goal of this project is to enable users of Memex to add/edit/remove comments in any page conveniently, while storing them in a standardised data model. This includes creating highlights or annotation of any text in an article and making them searchable for easier access.</p>

Extend the "Chart" functionality on the Study View Page by supporting additional types of charts such as line charts and area charts. Support chart toggle functionality to allow users to select different types of charts for the particular data set. Implement "group chart" functionality to improve UX for chart analysis.

<p>With this project, I aim to implement a fully functional command palette, that allows the user to access almost any function of the GDevelop IDE with a few keystrokes. I will also revamp the keyboard shortcuts of the IDE, adding support for shortcut customization and including shortcuts for other common actions that are currently missing.</p>

<p>The aim of the project is to improve the vega editor by adding support for settings panel , and improving upon features like uploading datasets and sharing visaualizations</p>

This project is to utilize the already existing revapi.org setup and expand it to properly detect and generate documentation for api breakages in a way that help users and extension writers. When this is done it will be a key central element in Quarkus releases and used heavily across all extensions. I'll enhance to the current revapi reporting, automate revapi usage in Quarkus CI build and document and script for daily usage of revapi.

<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>The objective of this project is to develop a new Sugarizer Measure activity which will work on Android/IOS platform and browser. The Measure Activity is a tool that allows kids to indulge in "learning by doing". It provides an interface for the kids to connect with the physical world and an opportunity to view and understand through a visual and statistical representation of the physical phenomena. Through this activity, children will learn concepts related to sound.</p>

cBioPortal allows submission of data sets to enrich its open-access cancer genomics database. Currently, new data sets can be uploaded to a separate repository for further review. However, to ensure full quality assurance, new data sets must be manually imported into an instance of cBioPortal and visually inspected to ensure the data displays correctly. This manual step is tedious, and presents a barrier to easily reviewing new submissions. To resolve this bottleneck in the review process, the proposed solution will create a new workflow that will trigger upon a new submission to automatically deploy a live staging instance of cBioPortal, with the new data set already imported. Time permitting, a second potential workflow could also be explored to further streamline the process by generating resources such as screenshots for easier visual inspection. These improvements would allow cBioPortal maintainers to more easily validate new submissions, leading to faster approvals for new data, and a higher quality database for cancer researchers.

<p>Mapping free text trait names to ontologies so that they can be processed is an important task that is not yet standardized. The goal of this project is to create an easy to use web application so that the curators can do this job efficiently.</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.

Flotta Operator is a Kubernetes operator used to manage the workloads of the IoT edge devices via Kubernetes API. Flotta workloads running on low-resource devices like RaspberryPI, Nvidia Jetson Boards, etc. These devices can be located anywhere, under so many circumstances which introduces many problems that affect the performance of the network. The current situation is there is no example project for using Flotta which is making a barrier to adopting the Flotta Project. The project goals are twofold: Edge Example Application 1. Implementation of workload application that would run on a bunch of Flotta devices collecting video streams/pictures from webcam and/or getting other data from sensors. 2. Implementation of WebApp that runs in the Flotta cluster that presents the results of aggregated data from devices in a nice UI to help users get some insights from data. Sense the Internet Investigating the Internet network topology and measuring the performance of the network using devices managed by Flotta. This will be done by performing large-scale network topology discovery efficiently ( both at the IP level and at the router level), sensing the quality of the network using active probing tools like traceroute, ping ..etc, and presenting this data in clear graphs with filters on the WebApp that running in the cluster to help project users making better decisions. Deliverables Implement the workload app that is running on Flotta devices, with capabilities of 1. Reading & collecting from webcams and sensors. 2. Performing a large-scale network topology discovery. 3. Sharing collected data to the Flotta cluster. Implement a Web App in the cluster, with capabilities of 1. Present aggregated data from sensors and webcams in a nice format. 2. Present devices networks topology in graphs. 3. Present filters and Frontend functionalities to help users read collected data. Write Documentation for the Edge Example App.

<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>Rating facility is a fundamental part of any review system. So, the idea of the project is to add the rating feature to the present review system in CritiqueBrainz. The implementation of the idea is in accordance with discussions on CB-244 (JIRA) and IRC. The project will provide users ability to rate entities on a scale of 10. Furthermore, it will also allow to review just via rating i.e no text needed (CB-247).</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>

<h3>Synopsis</h3> <p>WellcomeML is a python package containing a set of utility functions that use machine learning for reading, processing, embedding and classifying academic text data like publications, grants, and other documents. The need for developing a new feature for expanding WellcomeML with further visualisation modules has emerged; in this specific case the objective is to create a standard interactive visualisation tool for the results of the clustering algorithm present in the library.</p>

<p>The main aim of the project is to implement casbin technology in C++. Hence, it boils down to porting the existing fully functional Golang implementation to C++ implementation. Setting up the right permissions is just as important as using a secure authentication method. Without dictating what users can see and do, your information is as unsafe as if there were no first layer of authentication at all. Authorization occurs with every request the user makes, starting with logging into their account.</p>

With the help of JavaScript and HTML5/CSS, 1. Maintain musicblocks v3 issues Detailed discussion on all the existing features, issues and other resources of music blocks with the mentors, strategize and prioritize maintenance work accordingly and deliver a reasonably robust version. 2. Resolve issues of browser changes i.e. Planet's cross origin errors By reading the updates on chromium versions (Browser Security) there are a lot of websites facing issues to cop-up. However, it can be easily solved by the help of tutorials , brainstorming and better characterization of code. 3. Better characterize some music utils code to resolve the regression No regressions will be found by the end of the project in any music utils code. Pulling the latest bits of tone.js file in the repository will ensure that the problem is solved. 4. Update the documentation The document too needs updating to the latest versions of code changes , my experience of writing scientific research journals will ensure a finalized documentation by the end of the my term. 5. Add feature enhancement and solve other issues with musicblocks version 3. During the period of gsoc there are many possibilities of new a idea implementation or any unknown error detection during the continuous process of discussion and evaluation with mentor. In such cases , I am ready to work on that as my project size is medium and I am ready to give extra hours to ensure completion of the project while ensuring it's quality.

<p>Over 100,000 people have already been genotype through DTC genetic testing however, these data live in siloes, often inaccessible to the public. {Bastian Greshake, Philipp E. Bayer, Helge Rausch, Julia Reda, openSNP: A Crowdsourced Web Resource for Personal Genomics, 2014}. openSNP seeks to solve this problem by allowing users to upload their results, where they'll be freely-available for all.</p> <p>In addition to these genetic data, openSNP's broader goal relates to all types of quantified-self (QS) information as this is of interest to genetic researchers.</p> <p>So far, openSNP allows people to link their Fitbit accounts, thereby donating their activity, sleep, and weight data to the public domain. By now, there are many more tracking devices (HTDs) around, and many of them offer their APIs. By exploiting these services, openSNP can dramatically increase the amount of QS data available in the public domain, providing a means for academic researchers and scientists to find new associations. These associations are easier to find in openSNP than similar services since a user's genetic test results, their tagged phenotypes, and HTD data are all linked to a single person.</p>

Enhance the usability of API Dash by extending its compatibility to Android and iOS platforms, while introducing essential features such as environment variables management, request history, and collection runners with monitoring. By providing mobile compatibility, developers will seamlessly access API Dash features on their smartphones and tablets, enhancing productivity and workflow. The addition of environment variables, request history, and collection runners with monitoring significantly boosts API Dash's functionality, empowering developers with comprehensive testing capabilities and streamlined workflow management. Adapting the desktop version's features into a mobile interface optimized for limited screen space ensures that API Dash remains intuitive, user-friendly, and accessible on both Android and iOS platforms.