Think About Your Audience (with Bioconductor)
Tags: opensource, outreachy, beginners, bioconductor
Published: 2023-01-10 13:39:51

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:

1. Annotation
2. Data management and organization
3. Differential expression
4. Analysis of microarray data
5. Visualisation and normalisation of microarray data
6. 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](https://bioc2022.bioconductor.org/) conference in North America, the regional meetings in Europe ([EuroBioC](http://eurobioc2019.bioconductor.org/)), Asia ([BioC Asia](https://bioconductor.github.io/BiocAsia/)), and summer schools (e.g., [CSAMA](https://www.huber.embl.de/csama2019/)).

## 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](https://bioc-community.herokuapp.com/), [the Support site](https://support.bioconductor.org/), [Bioconductor website](https://bioconductor.org/) and the [YouTube channel](https://www.youtube.com/user/bioconductor).

## 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](https://github.com/Bioconductor/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](https://pandoc.org/) 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](https://www.lua.org/) 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](https://www.r-project.org/) 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](https://www.latex-project.org/) and [Pandoc](https://pandoc.org/) 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!