It’s really easy to get side-projects as a bioinformatic student. Although it is exciting to have a side-project to work on for the possibility of co-authorship or any possible reward, it is more important to be reallistic on the time commitment. Increasing the efficiency of the learning process is the topic I am currently focusing on. Especially when dabbling into a new realm of research topic, I always ended up with a lot of browser tabs without really getting the idea. I am documenting/trying/proposing the following workflow as getting the first crack of attempt to poke a new reserach project.

Before getting into the workflow, I want to briefly talk about some terms and idea: the core, the edge, and the utility.

the core

the classic

Find those old papers that you must cite, although they are using some terms in a different fashion and really hard to understand.

the different

When touching a new idea, we might be very excited but actually misunderstanding it. Try to find out what is making the topic really unique. Esqecially when a new idea is simply a less traveled path and not convoluted and complicated, chances are this is a way just don’t work.

the edge

Check out the newest paper to make sure you are with the state-of-the-art. What is the force that really pushing the field forward. It might be something from the upper level of science hierarchy. Simply working on application of techique migty be hot and interesting but also perishable. Beware of (self-claimed) destructional innovation.

the utility

Get some tools that can accelerate the general process. You can never get too familiar with software. In addition, consider writing down your own process just like this article, it helps to make thinking clear.

the note

Take awesome note that can go a long way instead of jotting them on a random receipt. I am using the inline board of to organize the above mentioned information. It is intuitive for me to organize every piece of paper as a little card while labeling them with some tags that fit in the context.

Another trending idea of knowledge management in 2020 is Zettlekasten Method, of which I think the main property is the linkage between note entities. I think it is worth mentioned but I personally have not really integrate it into my workflow. I think the main point of this method is actually the aid of forming long term memory while practicing it.

the version

Things might change as you get more familiar with things. You can version control everything on the computer. It might be hard to use the command line all the time. I suggest using GitKraken to aid this process. It is the best GUI for git in my opinion.

the workflow

the board

Open two inline board in, one for tools and one for information.

Group by certain properties that fit in the context. For the tool board, I group the cards of tools by self defined priority. Because as a bioinformatician at a tool trier stage, it might take some time untill we actually find the one that work. Besides, I tag each card with some random properties such as the programing language, aimming problem, or special techology it applied.

For the information board, I group the cards of papers or blog posts by years at the beginning. Then after gathering about ten non-redundant ideas, I will try to reorganize them according to certain properties that fit in the context and can help me find some insight.

the flow

After gaining enough idea of the field, now its time to plan actions. I used to rely on Notion for project managing, but several draw backs such as long loading time, learning curve for cooperators, and worth improving off-line mode made me give up this approach. Now I use Whimsical as my research whiteboard. It support flowchart, mindmap, sticky note, and even wireframe (in case you are gonna plan the front end of your new research software too).

I have not really use it with a team but I can easily share my idea or progress with supervisor or teammates. I use the comment function as a todo tasks queueing system. All of your comment will be listed on the right side of the page after you click on the toggle comment bubble on the upper right corner. So I can easily get an idea about what I should work for the next step.