InterMine

Mentors: Student: Akshat Bhargava

<p>The current Intermine’s viewer interface works on JavaServer Pages Technology and is planned to be discontinued in a few years. And, a new interface namely BlueGenes has already been developed. So, to allow developers to easily develop tools (any type of tool, visualisation, tables or anything that can be integrated on the gene / protein report page) for BlueGenes (the new interface), Intermine released a BlueGenes Tool API which defines specifications on how to build BlueGene compatible tool in JavaScript. Currently there exists two such tools - protovista and cytoscape-interaction-network-viewer. The BlueGenes ClojureScript application actually queries for all tools available before sending the report page to frontend and integrates the ones found. These tools are actually javascript applications following the specifications provided by the BlueGenes tool API and receive some initialisation input from BlueGenes like gene id in case of a gene report page. The purpose of this project is to develop BlueGenes compatible visualisation tools which can help biologists and explorers have better insights via the report of a gene / protein on the report page.</p>

Mentors: Student: Ankur Kumar

<p>Intermine is a powerful data warehousing, integration and analysis tool used to store and share genomics data. However, setting up an instance of Intermine is a time consuming and error prone process. It also requires technical knowledge and some familiarity with Java, Postgres and shell scripts. These issues create a barrier for entry and friction in the adoption of intermine by the bioinformatics community. To solve these problems, Intermine team is planning to create a cloud platform that offers managed Intermine instances. This will remove the technical burden from the user and greatly simplify the creation of intermine instances. Also, the work done on Intermine cloud can easily be translated to simplify the creation of Intermines locally. This project forms a part of the Intermine cloud project. It includes packaging of intermine and it’s components in docker containers, cloud infrastructure setup, orchestration of containers, authentication, and authorization on the cloud.</p>

Mentors: Student: Rahul-07

<p>In the current scenario, A user logs in the desired intermine and saves the results and the required data. The problem arises when the same user wants to access a different intermine, He/She will have to register again on this new mine and log in again. So , Currently Intermine community does not have a single common sign-in mechanism and thus it is authenticating users with the help of tokens (temporary and permanent one) or using google and Elixir services to log in. This project will modify the existing token mechanism by making the intermine as an OAuth2 provider with a single common Authorization server for all 30 mines so that user could access all the mines with the single set of credentials i.e just one time registration.</p>

Mentors: Student: deepak

<p>As Intermine is providing integrations with different biological data sources, Intermine has to work with different file formats to read data for the different data sources. In bioinformatics, many file formats are used for storing DNA and protein sequence information. Each file format has a formal specification and parser can be made by following the specification rules, But as most file formats are just simple text file that can be easily edited by anyone so its quite easy to make mistake and people may not comply with the standards while creating/editing file, that can lead to errors while parsing/or using that data.</p> <p>This project’s Idea is to create a standalone validation tool/library that can test the validity of a single or multiple biological file format. The project will provide full control over how one wants to perform validation, a user can use the project’s rich API to customize the behavior of the library. It will provide a generic validation library that can be further extended for any number of file format, A user can even provide its own validation implementation if he/she customize the behavior of the library.</p>

Mentors: Student: Prabodh Kotasthane

<p>Presently InterMine uses Struts framework which is outdated. InterMine provides RESTful web-services which facilitates to execute custom or templated queries, search keywords, manage lists, discover metadata, perform enrichment statistics and manage user profiles. The main objective of this project is to migrate the web-services from Struts to Spring framework and document the APIs with Swagger in compliance with OpenAPI Specifications.</p>