Outreachy Interview: Sakshi Srivastava on JavaScript data visualisations for BlueGenes

This is our blog series interviewing our 2020 Outreachy interns, who are working remotely for InterMine for 3 months on a variety of projects. We’ve interviewed Sakshi Srivastava, who will be working on data visualisations for BlueGenes.

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

Corona Namaste everybody! Delighted to be a part of the InterMine team. I’m an undergraduate pursuing Bachelor of Technology in computer science from Guru Gobind Singh Indraprastha University, Delhi, India. I’ve been working with JavaScript and the web ecosystem for the last 2 years. I like to take part in tech meet-ups and hackathons (also, have won a few of them). I like to solve puzzles that involve logical and mathematical questions. I’m also doing competitive programming to increase my problem-solving ability. I love to draw and paint, although I haven’t done it from the past few months, as it’s my best to escape from the real world and take a break from everything going on in life. I like to listen to soft relaxing music and play guitar sometimes. When I’m not on my laptop, you will mainly see me sleeping (mostly :P), delved into some interesting chat with friends, or day-dreaming. I’m in the phase of inspecting different kinds of technology sectors to discover the one which flatters me the most. One of my magnificent project in the field of data visualisation is IPLDataVizProject which was given in an interview as a task.

What interested you about Outreachy with InterMine?

Biologists study life on scales from single molecules to whole organisms to entire ecosystems. I’ve never explored the bioinformatics world much but getting acquainted with the science behind life always interests me. InterMine fits like a glove to me. Also, javascript is exactly where my interest revolves. I wanted to strengthen my skills and increase my capability to bring more and more conversions. Consequently, this perfect opportunity will give me a chance to get familiar with the underlying scientific notions by applying my computer science skills. But this is not the only reason that makes me choose InterMine. The primary reason was the optimistic environment at InterMine which never made me even go explore any other organisation during the application process. The mentors are highly admirable who always entertain the ideas, doubts, requests elegantly and motivate others to be awesome. The time spent with them discussing the details of the project was intriguing. They are one the most indispensable parts of the InterMine community.

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

The complexity of biological problems requires understanding and then analysis of networks and interactions. But when the data is huge it becomes difficult to get better insights easily. The aim of my project is to create different visualisation tools to propel the cluttered and chaotic data into an understandable form. This will help biologists to understand the networks and interactions between different entities in an easier way and consequently draw relevant conclusions with single sight to the graph.

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

As we know InterMine has tons of biological data worldwide. The procurement and comprehension of data are essential in order to mold it into meaningful visualisations and get better insights. I will try to get familiar with the biological entities prior to beginning each viz by studying the InterMine’s data models and with the help of mentors. This will help me to write better documentation or maybe it could light me with new viz ideas in my mind.

I also came up with an interesting idea to use storybook.js to showcase all our visualisation tools in one place for demo purposes without actually needing anybody to run the tools locally. I’ve started exploring monorepo techniques and how we can actually integrate it with our visualisation tools. This is going to be a new and engaging challenge for me as I’ve never worked with monorepos before. This is going to be fun.

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Roshni Prajapati on BlueGenes UX, user research, and saving people from bad design

This is our blog series interviewing our 2020 Outreachy interns, who are working remotely for InterMine for 3 months on a variety of projects. We’ve interviewed Roshni Prajapati, who will be working on UX research and recommendations for BlueGenes.

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

Hi team, can’t deny the wait for a totally new experience is driving me crazy here! I’m an IT undergraduate pursuing bachelors of Technology at IIIT Allahabad and will be onboarded to IIIrd year from August onwards. Primarily my interest lies in interaction design, user research, product thinking and a bit of graphics design still I don’t mind banging lines of code to build stuff that interest me. Few of my works could be seen here & here.

Some days I try to solve user issues by merging aesthetics, a bit mathematics & data in unequal proportions while other days I can be spotted preparing for my upcoming hackathon, lying all day watching cartoons or enjoying 70s-80s classical playlist. 

    Other than this I’m a wanderlust person, a guitarist, a painter, an intermediate football and Table Tennis player and a coffee addict 😛 

What interested you about Outreachy with InterMine?

I have this craving of improving things to redefine work for living breathing humans i.e,  to save them from bad design. Case with InterMine is that while surfing through the mine-sites I noticed it mostly comprises analytical data and their representation. The current website has several user issues & pain points, also naive look and presentation of the data is not apt and even violates some design rules. This made me dive deeper into the real world biodata and their visualization for better usability of the website added the fact that the organization itself registered a design issue (driving me more to work).

    One of the facts is that design analysis needs views from users and developers and it becomes important that the community interacts. So I needed a better understanding of the real world bio data (new to me) and mentors willingly helped, this everready response brought an optimistic vibe to work for the team and organization.

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

The content layout in the current website design needs to be strategically placed in order to make it easier for users to go through. Since the site contains heavy analytical and a variety of biological data, my task will be to organize the website content such that users can find the things at ease, improving overall user experience. So basically I would try to carry out my process in following phases-

Discover & Define: Carry out questionnaire sessions and meetings for collecting user experience observations then interpret the observations and define insights. I will try to convey my ideas through user personas & stories and finally set my design challenges.

Develop & Deliver: and further will discuss ideas and through sketching and experimenting and prototyping by working on feedback iteratively.

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

Previously I have worked on several projects of my own and this would be the first time I would be working with a community. So collecting user experience observations remotely through unit testing and other methods is gonna be quite a challenge for me. One of the major tasks also includes my contribution in implementation of design of which I’m concerned. Since this is gonna take some time, it could be counted as another challenge still I’m pretty much sure that work would get done under the time duration provided 🙂 

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Outreachy Interview: Pooja on the CLI tool for managing InterMine instances

This is our blog series interviewing our 2020 Outreachy interns, who are working remotely for InterMine for 3 months on a variety of projects. We’ve interviewed Pooja Gaur, who will be working on the InterMine Boot CLI tool project.

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

Hello!! Excited to join the Intermine team. I am from Ajmer Rajasthan, India. I am pursuing MS by research from IIIT Hyderabad, India. I have completed My btech Honours from Govt. Women Engineering College Ajmer, Rajasthan. After that I worked for two years in a startup, where I worked on automating common queries by pattern matching. Right now, I am a Research Student in the Data Science and Analytics lab at IIIT Hyderabad. My current research work deals with increasing revenue and user satisfaction for retail stores. My interest varies from research in data organization, data mining and analytics to web development. I developed interest in open source after participating in Hacktoberfest 2019. I came to know about Outreachy from one of my friends in college. I like dancing and visiting new places. I used to take part in regional dance competitions before joining college. 

What interested you about Outreachy with InterMine?

I was browsing the past projects on the outreachy site. From a coarse look, I shortlisted around 7 to 8 projects. The intermine’s documentation was clear for contribution, So I started digging deeper and developed more interest over time in this organization. I liked the idea of providing tech power to biologists to improve their work flow and ease their work.

When the projects list was out, I saw the making CLI tool project. I had manually set up the intermine which is a laborious process and I realised that this project would be very helpful for end users. Also my current knowledge is aligned to this project, and it would be helpful in extending my knowledge.

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

My project is Create a CLI tool for managing InterMine instances. Building an intermine is a laborious process and requires a lot of system knowledge. But every user may not have deep knowledge of the system. Intermine Boot is part of the Intermine Cloud project. Intermine boot is a convenience tool which provides a single command setup to easily create and manage the intermine instances locally. Along with local instance creation the project supports building instances inside the docker container for e.g to use in Continuous Integration.

My aim is to extend the intermine boot to implement the Continuous Integration use case. Here, a CI pipeline will be written (using travis) and a docker image will be created which can be loaded during CI pipeline to run tests. Along with it, I will integrate wizard and configurator with intermine boot to ease the configuration and setup of local instances of Intermine.

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

Although I am comfortable with python scripting and development, my experience with docker and continuous integration is minimal which could create a steeper learning curve.

To overcome these issues, I have already started digging a little deeper into project requirements and pick up required knowledge for docker and continuous integration.

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Outreachy Interview: Qian on the InterMine Training Portal

This is our blog series interviewing our 2020 Outreachy interns, who are working remotely for InterMine for 3 months on a variety of projects. We’ve interviewed Qian, who will be working on the InterMine Training Portal.

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

Hi InterMine team! I feel so excited to be part of the team! I am a Computer Science undergraduate from National University of Singapore. Next semester I will be a sophomore. I transferred from Shanghai Jiao Tong University to NUS last year. Previously, I majored in chemistry and biology. So I have some biology background. I feel so happy to take advantage of both my major backgrounds to contribute to InterMine!

I did an HTML-related project last semester. This is the link. This is the pr I cooperated with my partner. We dealt with generating an HTML textbook in seconds which is our introductory book to programming. I learned Java and JavaScript this year. I also helped a professor to deal with huge data using Jupyter Notebooks last semester, from which I learned python. (To be frank, python is much easier than Java. I was so frustrated by Java final :(. )

I am a newbie in computer science. I feel very lucky there are many open CS resources  to help me learn basic concepts. And, open source platforms are good places to find people with similar interests. I learned much from InterMine discord chat!

Apart from studying, I love playing the piano. My biggest goal is to be able to play La campanella fluently. This is my favorite version.

What interested you about Outreachy with InterMine?

Among many projects, this project almost does not restrict anything. I can design the portal according to my own ideas (of course I get advice from mentors). This is my first internship so I want to try to be more flexible.

Another reason is InterMine is about biology data processing. I have a biology background and I am interested in genes. I think cooperating with computer science, especially data analysis, is the future of biology.

Further, I love the atmosphere in this community. Yo is a good mentor as she is so helpful and kind. Members in InterMine are all warm-hearted and enthusiastic about new ideas. I learned much during the application period, especially during this hard period. I got mental relaxation when communicating with people in InterMine!

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

  1. Change the layout of the training portal page to be more useful and beautiful. 
  2. Make text and video tutorials for different languages.
  3. Add some features to the page.
  4. Combine different tutorials together. 

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

I have to rewrite tutorials in different languages which I am not very familiar with. So I am learning Perl and R these days! 

Another challenge I think I will meet is I am not sure about the time arrangement. As this is my first internship, I don’t have experience in arranging a schedule by myself previously. I hope to finish as I wrote in my plan. To overcome it, I am going to get advice from my mentors and volunteers. As this is a 3-month internship, I think I can have better anticipation of productivity with the guidance of mentors after 2 or 3 weeks. Then I will adjust my plan timely.

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Announcing the InterMine 2020 Interns 🚀

Announcing the InterMine 2020 Interns! 🚀

As we mentioned in an earlier blog post, this year InterMine is participating in Outreachy for our May-August (northern hemisphere summer) internships. This year we’ll have five Outreachy interns, as well as a couple of in-house interns working with us. Please give them all a huge round of congratulations! 

Our interns and their projects 👩‍💻👨‍💻

InterMine training portal – Qian

Qian will be working on the InterMine training resources, creating new programmer and UI-oriented tutorials and updating/organising existing tutorials. 

Qian will be mentored by Yo and Asher. 

CLI tool for managing InterMine instances – Pooja Gaur

Contributing to the InterMine cloud project, Pooja will be orchestrating better automated builds for InterMines that will also work nicely in Travis or other CI. 

Pooja will be mentored by Kevin and Ank.

Improving the UX and UI of BlueGenes – Roshni Prajapati

BlueGenes, the new InterMine UI has improved drastically since Kevin joined the team and began adding and improving features. Roshni will conduct research into the usability and UX of BlueGenes, and redesign / improve interfaces where needs are identified. 

Roshni will be mentored by Yo and Kevin. 

Improving the InterMine Data Browser – John Mendez

The InterMine Data Browser was a 2018 GSoC project led by Adrián, designed to make it easier for people new to Intermine to learn and explore what types of data are present in an InterMine. John will be helping update the Data Browser with new features and migrate it to React. 

John will be mentored by Adrián, Nikhil, and Aman. 

Javascript Data Visualisations – Sakshi Srivastava

Last year, Akshat Bhargava created a suite of data visualisation tools for BlueGenes. Sakshi will be extending this work, refining some of the Tool API specifications and adding new data visualisations. 

Sakshi will be mentored by Akshat,  Kevin, and Asher. 

With thanks to our sponsors

We’re grateful to the Wellcome Trust for awarding a Diversity Enrichment grant that enabled us to sponsor three Outreachy interns, as well as Outreachy themselves who were able to sponsor another two internship positions.  

In-house interns  

We’ll also be working with Ank Kumar (working on InterMine Cloud related projects) and Celia Sanchez Laorden (InterMineR). 

What about GSoC? 

In previous years we also participated in Google Summer of Code – this year InterMine wasn’t accepted as a mentoring organisation. It is common for GSoC to “rest” applicants occasionally, so we’ll continue to apply and hopefully we will be back in GSoC next year.

Once we knew we weren’t accepted into GSoC for 2020 we joined the Open Bioinformatics Foundation GSoC org, who act as an umbrella organisation for GSoC mentoring organisations, and we had several strong applicants apply via the OBF’s organisation. Unfortunately the number of slots awarded to the OBF was lower than the number of promising students the OBF was ready to accept. This meant that InterMine was unable to take on any GSoC students, even though there were high-quality applications.