Call recording available: GSoC 2019 Final Presentations

Our Google Summer of Code students presented their work at a special edition of the community call yesterday. You can catch up on the entire recording on YouTube – or scroll down to see individual presentations. The agenda and notes accompanying the call (including code and slides links) is in Google Docs.

Prabodh Kotasthane – Spring Migration

Prabodh’s presentations starts at 3:54: https://youtu.be/ZzV6JmVRQmA?t=234

Slides

Ankur Kumar – InterMine Cloud

Ank’s presentation starts at 13:12: https://youtu.be/ZzV6JmVRQmA?t=792

Laksh Singla – Upgrading imjs & im-tables

Laksh’s presentation starts at 21:08: https://youtu.be/ZzV6JmVRQmA?t=1268

Rahul Yadav – Single Sign-In

Rahul’s presentation starts at 27:39 https://youtu.be/ZzV6JmVRQmA?t=1659

Deepak Kumar – InterMine Schema Validator

Deepak’s presentation starts at 24:11 https://youtu.be/ZzV6JmVRQmA?t=2051

Akshat Bhargava – Data Visualisations

Akshat’s presentation starts at 41:30 https://youtu.be/ZzV6JmVRQmA?t=2490
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14 August: InterMine Community Call and Google Summer of Code Final Presentations

After weeks and weeks of fabulous work, our six Google Summer of Code projects are approaching the finish line. As in previous years (2018, 2017), our students will be sharing their work in a series of 5-minutes presentations at an InterMine Community Call. Everyone from the InterMine community is encouraged to come and see what our fantastic students have been up to.

Joining the call

The call will be on the 14th of August 2019. (Note we previously advertised the call as being on the 15th; this was an error – the call is definitely on Wednesday the 14th of August).

Time: 17:00 UK time / 21:30 IST / or check your time zone here: https://arewemeetingyet.com/London/2019-08-14/17:00/Final%20presentations

Agenda and joining instructions: https://docs.google.com/document/d/14KAdYACPowLxcIhOe6yVzeYsHMnSy2X0WzuJ124KZ30/edit#heading=h.x7mc3otkj1bu

Here’s a sneak preview of what our students have been working on:

Status update for BlueGenes

It’s been a while since we posted our last (rather optimistic) update around BlueGenes, so we thought we’d share a quick update, starting with the basics.

As a reminder, the long-term goal of BlueGenes is to replace the existing JSP-based UI with a more modern interface – one that works well with mobiles, one that hopefully responds more quickly and is easier to use, and perhaps most importantly, is easy to update and customise.

Some of the questions we’ve had in the last few months:

Q: Will BlueGenes replace the current JSP UI?

A: Yes, eventually. Once we reach official beta/prod release (we’re currently in alpha), we anticipate running them concurrently for a couple of years, but we probably will only provide small fixes for the JSP UI during this period, focusing most of our development effort on BlueGenes.

Q: Do I have to run my own BlueGenes, or can I use the central one at apps.intermine.org?

A: Since BlueGenes is powered purely by web services, it will probably be possible to run your InterMine as a server/api-only service and use BlueGenes at bluegenes.apps.intermine.org/. You can also run your own BlueGenes on your servers and domains, allowing you to customise it so it’s suitable for your data, and not having to rely on our uptime. Either (or both) should work fine. There will be some version requirements related to what version of InterMine can access all the features of BlueGenes – see the next point.

Q: What version of InterMine do I need to have to run BlueGenes?

A: BlueGenes will require a minimum version of InterMine to run. The original release of InterMine web services focused primarily on providing a way to give JSP users access to their data programmatically, but at the time there wasn’t an anticipated need for application level services such as superuser actions. There are a few web services and authentication-layer services we still need to implement, so it’s likely BlueGenes will need API version 31+ or higher in order to be fully-featured. InterMines with API version 27 or higher can run a basic version of BlueGenes. You can check out this table to see if your InterMine is configured to work with BlueGenes.

Q: Ok, so what’s left to do before BlueGenes is released as a public beta?

A: Mostly authentication, superuser and MyMine features – things  like saving and updating personal templates, sorting lists in folders, updating preferences and passwords. Some of these features require updates to InterMine itself in order to work – hence the minimum version noted in the previous question. Once these are ready we’ll move to the public beta stage.

Your input here will be incredibly welcome, too – the more feedback we get early on, the more polished we hope BlueGenes can be.

Q: Will BlueGenes work nicely with HTTPS InterMines?

A: You will be able to run BlueGenes without HTTPS, but in order to avoid inadvertently exposing user passwords, the login button will only be available over HTTPS connections. We’re also working with a student over the next few months, to implement a pilot InterMine Single Sign On service. You can read about it in our interview with Rahul Yadav.

Q: Will I be able to customise the way BlueGenes looks?

A: Totally! There are two ways you can do this. One is to make sure you have your logo and colour settings configured in your web properties. We have a nice guide for that. This’ll tell us what your preferred highlight colours are – FlyMine is purple, HumanMine green, etc. If you’re really dedicated and would like to write your own CSS, you can do that too, if you’re running your own InterMine/BlueGenes combo.

Q: I have some nice custom visualisation tools in my InterMine. I don’t want to have to re-write them!

A: We don’t want you to re-write them either! It depends how they’re implemented in your mine, but we’ve designed the BlueGenes Tool API with you in mind, and many Javascript-powered tools will require only a few lines of code to become BlueGenes ready.

As an example, the Cytoscape interaction viewer currently used in some InterMines only requires 20 lines of code to import into BlueGenes, plus a few lines of config – all the other files (and most of the config too) is boilerplate that we auto-generated.

Community outreach call coming up – 6 June, all welcome!

Update: If you missed the call, the recording is available on YouTube

InterMine runs quarterly Community Outreach calls, targeted to interest people in the overlap between life sciences, open source, and open science, with a few InterMine specific updates sprinkled in as well. Most times we host one or two guest speakers who work in scientific outreach or have done an interesting InterMine-related project we’d like to spotlight. We aim to welcome anyone interested in community outreach and generally try to avoid overly techie themes.

The next outreach call coming up on June 6th, 5PM UK time, with two exciting guest speakers, plus we’ll briefly mention the six Google Summer of Code students working with us over the next few months. 

Please help to spread the word by sharing with colleagues and friends – the more the merrier!

Speakers:

  • Malvika Sharan is a computational biologist and a community outreach coordinator for EMBL Bio-IT, which fosters a community of bioinformaticians. She will be talking about inconclusiveness in Open Science Communities using examples from her work at EMBL and her involvement in The Carpentries, SSI, and Mozilla.
  • Emmy Tsang: I’m the new Innovation Community Manager at eLife and am now running the eLife Innovation Initiative. I’m going to talk about the #eLifeSprint– our effort to drive and support collaborations in developing open-source software for open science, and the latest developments of Reproducible Document Stack project, which include a roadmap towards sharing reproducible research.

Agenda and joining details: https://docs.google.com/document/d/1VhfFbOwx95UZP-sRDVib8HNGPCXCfnpDVGh8VAbeI0c/edit – we’ll be using Zoom for this call, rather than GotoMeeting.

When: 6 June, 2019 at 17:00 UK time / or in your timezone: http://arewemeetingyet.com/London/2019-06-06/17:00/InterMine%20Community%20Outreach%20Meeting

GSoC Interview: Akshat Bhargava on new data visualisations for BlueGenes

This is our blog series interviewing our 2019 Google Summer of Code students, who will be working remotely for InterMine for 3 months on a variety of projects. We’ve interviewed Akshat Bhargava, who will be creating data visualisations for BlueGenes.

Hi Akshat! We’re really excited to have you on board as part of the team this summer. Can you introduce yourself?

akshat1Hi InterMine team, I’m very excited too for this upcoming summer! I’m a Computer Science undergraduate going to start my 3rd year this August. I’m primarily a Javascript Developer (Web & Hybrid Mobile) and have been working with it for the last 2.5+ years, but the real me is a person who loves to solve problems in general, may they be related to programming or not. I’ve been exploring the field of data visualization for the last few months and I am in love with it. Have a look at IPL (cricket) data viz I created a few months back here.

Apart from coding, I love reading about psychology, history and watching horror movies.

What interested you about GSoC with InterMine?

I feel it magical how numbers show their true faces when seen via a meaningful visualization, and this is why I’m most excited for this summer with InterMine.

Real World Bio Data + Data Viz = Something big coming in! ❤

Another reason for my interest in InterMine, is that I applied to InterMine last year too for Cross InterMine Search Tool and couldn’t make it, but understood it’s community and how they work. The mentors are very helpful and supportive to everyone, so I directly jumped here this year. 😀

Tell us about the project you’re planning to do for InterMine this summer.

InterMine has tons of different types of biological data, this summer I’ll mostly be working on discussing and developing visualizations for data, making it easier to biologists to understand it in a easier way, and draw relevant conclusions with a single sight to the graphs.

There is a software called BlueGenes, which is already developed and helps explore different mines, it provides a tool API which allows Javascript developers to create additional visualization tools on top of it, which can be integrated on any Gene or Protein result page. My goal for this summer is to create a different variety of such visualization tools in order to enrich the visualization of different types of data.

As an example of how useful is what I’m doing, one of the visualizations I’ll be developing will help us understand how the expression of a particular gene is distributed among different tissues. This information is helpful for cancer biologists that want to assess if a gene is highly expressed across different tissues of an organism, because that gives a relative picture on to what degree it’s implicated in diseases.

Are there any challenges you anticipate for your project? How do you plan to overcome them?

Data visualization is something that requires you to understand the data properly first in order to be able to actually create some meaningful visualization out of it, and since I’m not very familiar with InterMine’s data model and the related biological terms, I’ll face some difficulties during my thought process of “what and why” to visualize. To overcome this, I’m already exploring more and more of the InterMine’s data model, trying to understand how to deal with different types of data, and how to create the appropriate visualization for them. Mentors are really helping me out with this (overall in terms of tech, viz and everything). 🙂

Share a meme or gif that represents your project

akshatmeme1

GSoC Interview: Migrating from Struts to Spring with Prabodh Kotasthane

This is our blog series interviewing our 2019 Google Summer of Code students, who working remotely for InterMine for 3 months on on a variety of projects. We’ve interviewed Prabodh Kotasthane, who will be working on a project to migrate InterMine’s RESTful web services from Struts to Spring.

Hi Prabodh! We’re really excited to have you on board as part of the team this summer. Can you introduce yourself?

I am a final year Computer Science Engineering (B.Tech.) student from Birla Institute of Technology, Mesra, India. I have been coding in  JAVA and related frameworks, C/C++ and python since last 4 years. I have contributed to Open Source Community, some software development projects and hackathon projects at college level. Prabodh
I successfully completed GSoC 2018 with OpenMRS. My project was OAuth Module Enhancement and SMART Apps Support. Details about the project can be found here:

https://pkatgithub.github.io/GSoC-2018-Final-Evaluations/

Presently I am doing internship under Microland Limited, Bengaluru, India till end of May 2019. Here I am working around graph databases and technologies like Apache Kafka and Neo4j with all the coding part done in python.
Apart from coding, I have many other interests and hobbies which include singing, cooking, photography, fine arts, basketball and writing.

What interested you about GSoC with InterMine?

It was around mid Jan this year when I got to know about InterMine.
Previously, I have worked with Java Spring Framework and hence I am comfortable with the same. So, I was searching for GSoC organisations which have something to do with Spring and then I got to know about InterMine and their project in which they were planning to migrate the web-services from Struts to Spring.
I read more about InterMine and also about the project, and I found it interesting. I went through the documentation of the project and joined the discord handle of InterMine so that I could connect with the mentors and the community.
I had a warm welcome into the community. Julie, Daniela and Yo are always excited to chat and exchange thoughts and it’s been such a good time with them till now.
All in all, this community, this project and the people associated to this project made me believe that I can do a GSoC with InteMine!

Tell us about the project you’re planning to do for InterMine this summer.

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.
Spring framework is evolving all the time and is more robust and flexible as compared to the Struts framework.
OpenAPI specifications are easy to write and Swagger Codegen, which supports Spring, makes the job of developer easy by generating the code stubs which can be modified to render the services.

Are there any challenges you anticipate for your project? How do you plan to overcome them?

InterMine has a lot of web-services, a total of 70, with various different functionalities.
The business logic of web-services is strongly dependent upon the
classes in webcore and in order to migrate a web-service, the knowledge of underlying logic layer is a must.This is going to a real challenge. It is a requirement to give proper time and understand this business logic layer of the project.
Apart from this, writing tests is also a time taking job. I wish I could get some help in that! 😛

Share a meme or gif that represents your project

PrabodhMeme

GSoC Interview: InterMine Schema Validator with Deepak Kumar

This is our blog series interviewing our 2019 Google Summer of Code students, who working remotely for InterMine for 3 months on on a variety of projects. We’ve interviewed Deepak Kumar, who will be working on the InterMine Schema Validator.

Hi Deepak! We’re really excited to have you on board as part of the team this summer. Can you introduce yourself?

Hi, Thank you for this opportunity, Let me first talk about myself, My name is Deepak Kumar, I live in Ahmedabad, India with my family. I started coding when I was in 17, I had two great teachers in my school days who introduced me to computer programming, and from that time I got interested in this field.

I completed my graduation in Computer Applications from St. Xavier’s College, Ahmedabad and currently I’m doing  Post Graduate Program MSC.IT(Information Technology) at DA-IICT, Gandhinagar, India.

Now talking about my technical details, I love working on challenging projects, I’ve worked on several projects, One of my favourite project that I created while pursuing my bachelors was ‘Smallscript’, It’s a compiled programming language that compiles to bytecode and runs on JVM that makes it platform-independent. It’s my favourite project because It was challenging and when I started with the project I didn’t know any technical detail about compilers, so I had to start from very scratch.

I’ve also worked with a startup company, where I worked as a backend-developer with a team of 8 people and our team was really fantastic, I worked on two projects there, and I really enjoyed it, working with a big team wonderful experience.

I’ve recently started my open source journey with GSoC 2019. Though I’m new to open source, I’ve started contributing to ‘JabRef’ and as I’m selected for GSoC 2019, I’m also going to work with Intermine this summer, and have future plan to contribute to Intermine after completion of GSOC. I also regularly participate in coding contests and hackathon, In one of the AI contest, I built an AI game that ranked 68 among thousands of participants.

Currently, I’m working at OpenXcell Technolabs as an Intern, which is part of my MSC.IT Master’s program. I love reading, travelling, table-tennis and working with new technologies.

What interested you about GSoC with InterMine?

When GSoC 2019 was about to start, I had already bookmarked a few of the previous year organizations I was interested in, and hoping that Intermine will be part of GSoC 2019 too. When the organization list came out, I was super excited to see Intermine in the list. After going through the Intemine’s idea list, I found myself very interested in ‘Intemine Schema Validator Project’, So it was really the Intermine’s project that made me interested in the community.

Tell us about the project you’re planning to do for InterMine this summer.

I’ll be working on a project named ‘Schema Validator’ for Intermine this summer. Well, the project is quite simple to explain, it’s going to be a library that takes a file as input and outputs whether that file is following a particular schema or not. While working on the project my goal from the first day would be to create this project as general as possible, so that the project can be easily extended to support other schemas as well.

Are there any challenges you anticipate for your project? How do you plan to overcome them?

Yes, there are few challenges that I will face while working on this project, One of the biggest challenges which I’m currently trying to solve is about performance. As the purpose of this project is to validate schema files, then the problem is how will I handle larger files that are filled with the content of like 10GB or more. I need to discuss this problem with my mentors that what is their expectation about the performance of the library.

Currently, I’m thinking about the solution to this problem. Maybe I can boost the performance by concurrently running multiple instances of a Schema Validator, Although it doesn’t matter how I implement it If the library is validating a 10GB file that it is definitely going to take a little amount of time.

Then there are also a few challenges regarding the implementation of the schema rules.