DEV Community: BerylKanali

Think About Your Audience (with Bioconductor)

BerylKanali — Tue, 10 Jan 2023 13:39:51 +0000

Welcome....again!
In this blog, I will explain the Bioconductor project and my experience contributing to my Outreachy internship project so far.

The Bioconductor Community

Bioconductor is a project spanning twenty years of continuous contributions to fields ranging from biomedical data sciences to immunology, microbiology and most recently single-cell genomics.

Bioconductor is a community made up of Data scientists, developers, scientists and many other people from all backgrounds and experience levels.

What Problem is Bioconductor Solving

In the past years and decade we have seen a huge change on how people view data and what data can do for us in terms of solving problems, innovation and technology in general. For us to understand data we have to analyze data and see what information we get or try to answer a question.

The aim of the Bioconductor project is to develop, support, and disseminate free open source software that facilitates rigorous and reproducible analysis of data from current and emerging biological assays.

How does your project fit into the community

The Bioconductor has helped the community by releasing packages
that are used for:

Annotation
Data management and organization
Differential expression
Analysis of microarray data
Visualisation and normalisation of microarray data
Storage and retrieval of large datasets

As of 2023 Bioconductor has:

2183 software packages
416 experiment data packages
910 annotation packages
28 workflows
8 books

On top of that, Bioconductor holds regular events that bring the community together, the annual BioC conference in North America, the regional meetings in Europe (EuroBioC), Asia (BioC Asia), and summer schools (e.g., CSAMA).

Why use Bioconductor

If you are a person interested in Bioinformatics, data science, open source software development, biological sciences and anything that cuts across the above topics, you might use Bioconductor in your work.

Bioconductor strives to update and manage all the packages in the best way possible. With Bioconductor you can get support from community members and also contribute to the project yourself.

You can get support or resources through the Slack workspace, the Support site, Bioconductor website and the YouTube channel.

Why I am excited to work in my project

Since I began gaining interest in Open Source, I think of accessibility as something that is very important. With technology changing and advancing day in day out, communities and organizations also have to advance and change to meet certain needs and demands. Being able to refactor documentation that have been written long time ago and update them and put them in a format that is easier to access and use is a huge accomplishment for me. I am excited to take part in the advancement and change happening in Bioconductor and open source as we try our best to make sure documentation and code is accessible, easy to understand and easy to use.

My project is Sweave2Rmd, which is a project to convert all Bioconductor Sweave vignettes to Rmd.

New concepts learnt

So far I have interacted and learnt some pandoc and Lua which I had not used before.

Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. Pandoc can convert between numerous markup and word processing formats, including, but not limited to, various flavors of Markdown, HTML, LaTeX and Word docx.
Lua is a lightweight, high-level, multi-paradigm programming language designed primarily for embedded use in applications. Lua is cross-platform, since the interpreter of compiled bytecode is written in ANSI C, and Lua has a relatively simple C API to embed it into applications.

Bioconductor uses the R Statistical Language and it has been great learning new things and applying my knowledge of R to the project.

I have also learnt how Bioconductor works and how people in Bioconductor collaborate as open source drivers. Being over 20 years old, they must be doing many things right and it is great just to experience that and learn from everyone.

What I found confusing in my project

In my first two weeks, I found almost everything confusing. I had not interacted with Latex and Pandoc that much before. Given R is an older programming language and the code was written long ago, syntax was different for some elements and I had to learn what some things mean, how they were done before and how they are done now.
The good thing is, as human beings one of our super powers is to learn, adapt to change and . That has really helped me throughout the internship till now.

I also have a very supportive mentor and other members of the project who are always willing to help. So far, I am enjoying working on my project and look forward to continue learning an contributing to it.

I hope you enjoyed this blog!

Everyone Struggles

BerylKanali — Mon, 09 Jan 2023 18:16:43 +0000

This is the second part of a series of blogs I will be writing as part of my outreach internship with Bioconductor.

In open source, most of the thing we do are learnt from others, the community or through research. When you start contributing to open source you are likely to meet new concepts, words, ways of doing thing and so on. Open mindedness will take you far in Open source. Being able to be open to asking questions, answering questions and seeking help whenever you need it, goes a long way in making your open-source journey easier.

When I started at Bioconductor, I struggled with several things. One of them was learning the language and context of sweave documents. R programming back then and now have different syntax and that was somehow confusing and made me struggle a bit.

Another thing was the different package names. In Bioconductor, there are so many packages available. Knowing which name was for a package, function or class was something I struggled with. I had to go back to confirm on the documentation many times just to start getting them.

I also struggled with asking for help. Sometimes I would get stuck and the spend a lot of time doing research and trying to solve everything on my own. This resulted to me spending more time actually struggling to get a solution when a solution was just a text away. I would have simply asked my mentor or community members.

How what did I do about my struggles?

Ask my mentor to help when I am stuck. I always ask questions or links to resources whenever I feel I need something. My mentor has really been supportive no matter how simple or hard my question is. I always get answer or recommendations on time.
Ask my community for help. Other members of the community may understand something very well and might be very resourceful with what you are struggling with.
Research. In open source, research is very important. Trying to figure out if there is documentation about something or how other people solved or overcame some of the things that you are struggling with. Using resources like Google search engine, stack overflow or cheat sheets can help.
Giving myself a timeline. If I struggle with something for more than a set period of time then next would to ask my mentor. This actually helped reduce time trying to get a solution by myself and enabled me do more work.

If you are struggling with a vocabulary or concept, it is good to first learn that all of us struggle with something. Next is to take action, you can use some of the methods I have shared and try figuring out what works for you. More importantly, you should try and understand why you are struggling with something. It might be because you are new to the concept or you need to learn a few things to help you understand things better.

Remember, everyone struggles!

My First Week as an Outreachy Intern with Bioconductor

BerylKanali — Fri, 09 Dec 2022 10:44:02 +0000

About me

My name is Beryl Kanali. I am an outreachy intern in the Dec 2022 to March 2023 cohort. I will be working on Bioconductor's project Sweave2Rmd project.

My interests are Open source, Data Science, statistics and technology in general.

Bioconductor

The mission of the Bioconductor project is to develop, support, and disseminate free open source software that facilitates rigorous and reproducible analysis of data from current and emerging biological assays.

Outreachy

Outreachy provides internships in open source and open science. Outreachy provides internships to people subject to systemic bias and impacted by underrepresentation in the technical industry where they are living.

My Motivation

I was introduced to open source in October 2021 when I participated in my first Open Source sprint, organized by Data Umbrella. Since then my interest in Open Source and Free software communities has grown.

After learning about outreachy, I decided to apply so that I can grow and get knowledge in open source. Given the magnitude of applications, I was honored to be selected and now experiencing what is it like to be an outreachy intern.

My Core Values

Curiosity and determination are the core values that have helped me get where I am today. I am always curious about how things work and how technology is used in different fields. That ishow I settled on Bioconductor as my project of interest.

Determination helped me get through all the stages of outreachy and finally get in.
These two corevalues come handy as I work on my project. There is a lot to learn at Bioconductor and from my mentors.

My first week has been nothing short of amazing. I am learning new things and meeting different people. I also get to contribute to a Free software project which is really cool.

What next?

I look forward to making the best out of my time in Bioconductor and learning as much as I can from my mentor. I am also excited to share my journey and lessons throughout my internship.