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Two short “Agile Bioinformatics” talks

April 12, 2013April 15, 2013Giovanni Marco Dall'OliomethodologyLeave a comment

I have just come back from the Programming for Evolutionary Biology course in Leipzig, version 2013!! The course is still going on, but unfortunately this year I could not stay the whole duration three weeks, as I have stuff to do here in Barcelona.

This year, apart from the “Introduction to Linux” module, I also taught a short module on “Best Practices for programming in bioinformatics”. It was pure fun, I think I never enjoyed so much giving a talk. I explained a part about Version Control, and another about Scrum, and people were really excited about it. To make you understand how much people liked this talk, consider that three persons invited me a beer after that, which for me constitutes the maximum compliment for a talk.

I have uploaded the two slideshow on slideshare. Unfortunately, the best part of the talk was a live demonstration on how I use these practices during my daily work, but at the moment I can not make these example publicly available. However, you should be able to follow the slideshows anyway.

Agile bioinf from Giovanni Dall’Olio

Version control from Giovanni Dall’Olio

Notes from a “Write it clearly” course

November 29, 2012November 29, 2012Giovanni Marco Dall'Oliomethodology, UncategorizedLeave a comment

I recently took a course on improving English Writing skills for researchers. These are my notes, organized as a series of “Do and Do not” lists, plus some separate list for each section of a research paper.

Feel free to have a look at them and make use of them. If you have any comments, you can add them here or to table. Have an happy paper writing day!

write it clearly — click to access the notes.

Gamestorming for bioinformatics

September 26, 2012September 27, 2012Giovanni Marco Dall'Oliomethodology1 Comment

Most meetings in academic research groups are awful. I have attended meetings that lasted hours and hours, and didn’t produce any useful output. I know researchers who try to avoid meetings as much as they can, and prefer to work by themselves, because of too many bad experiences. In the end, the problem is that scientists are not very good communicators, and most PIs are not trained for being group leaders, so meetings end up being very boring and time wasting, more harmful than useful.

Fortunately this year, thanks to a meetup group here in Barcelona, I discovered that there are many ways to improve meetings and make them more interesting. The most interesting is the concept of “Gamestorming”, which is based on transforming group meetings into “games”. If instead of inviting people to attend a meeting you ask them to participate to a short game, people are more likely to participate actively and make good contributions.

Most gamestorming techniques involve blackboards and post-its, and ask people to use them to explain their own opinion. A simple example of a gamestorming meeting would be a planning meeting where the group leader splits a blackboard into three sections, one for listing different “Project Proposals”, and the other two for “Pros” and “Cons” of each project proposal, and asks the participant to fill the blackboard using post-its. If you want to have a good overview of techniques for brainstorming in general, I can recommend you the book “Gamestorming“, by Gray, Brown, Macanufo, from O’Reilly, which I am reading these days.

In any case, I have been thinking about which planning “games” can be adopted in bioinformatics, or by researchers in general. Here is a list of a what I introduced or planned to introduce to my group:

Planning a 8-hours “Introduction to Linux” course with trello

March 9, 2012March 10, 2012Giovanni Marco Dall'Oliomethodology6 Comments

Next week I am going to give a 8 hours “Introduction to Linux” course at the “Programming for Evolutionary Biology” workshop in Leipzig. In this post, I will describe how I have used a nice planning software called “trello” to make the schedule of the course.

You must know that I am a big fan of using small card papers to organize things. I started using CRC cards from the ExtremeProgramming techniques, and now the way I organize my time is similar to the KanBan technique, although I kind of evolved it independently. In simpler words, I have the habit of cutting A4 papers into 8 smaller A6 papers, the size of a post-it, and use them to take note and to plan my projects. If you visit my office, it is full of collections of “A6” papers everywhere 🙂

One day I may prepare a blog post about how I organize my projects with A6 papers. For now, just consider that trello basically allows me to do on a web page what I usually do on paper. Also, trello allows to share workflows with other people on Internet.. For example, I can show you the schedule of the Linux course that I have made:

schedule for the Unix course on trello — my trello board for the "Introduction to Linux" course. Click to see it!

So, I used trello to make 5 distinct sets of cards, one for each of the 5 parts that compose the course. In each of this list, I filled some cards to describe the most important topics that I wanted to talk about in that part of the course. I have used some a red color label to highlight which is the most important message to transmit in each of the parts of the course, the “Take-Home” message.