Creation du script Shortstack

Running the Nextflow rnaseq pipeline

Often, one wants to download multiple FASTQ files from the NCBI Sequence Read Archive.

Often, one wants to calculate the sequence length from a FASTA file.

The NCBI partially non-redundant reference nucleotide collection (nt)

To download files from an URL when located on crunchomics or any other HPC server:

Since I often do this operation in a for loop in bash, I thought it would be handy to store it here:

I have recently helped a colleague to add the curve from a nls model to its ggplot.

Because of these corona-days, I have made and sent around a list of useful online resources to learn programming and data analysis using R and Python. I hope it is useful for others as well.

I have done this so many times but without actually remembering how to do it properly. So here’s my personal note on how to do it. I took inspiration from the Github guidelines.

This is a speed-blog post written upon a workshop held at the CarpentryConnect 2019 conference in Manchester.

You’ve downloaded your favorite (plant) genome, but you’d only want to have chromosome 1 for instance. Let’s suppose you’re working on tomato so you’d need to extract everything between SL4.0chr01 and SL4.0chr02.

Summary

I had the chance of writing a small article for the Amsterdam Science Magazine that “aims to be a platform that displays the enormous creativity, quality, diversity and enthusiasm of the Amsterdam scientific community. It offers early career scientists (MSc students, PhD candidates, postdoctoral fellows), as well as more advanced researchers, the opportunity to communicate their latest and most interesting findings to a broad audience”.
I explained the origins and goals of the Amsterdam Science Park Study Group for a broader audience! I am grateful for this nice opportunity.

Summary

I got invited by the Graduate School Experimental Plant Sciences (EPS) to give a lecture on data management scientific programming and good practices. While mostly aimed at bioinformatics, it is far from being restricted to genomics. The presentation I’ve shaped was intended to give a good overview of what needs to be learned by the newest generation of life scientists.
You don’t have to be an expert in code to actually benefit from better code and data know-how and good practices!

Summary

I got invited by the Graduate School Experimental Plant Sciences (EPS) to give a lecture on data management scientific programming and good practices. While mostly aimed at bioinformatics, it is far from being restricted to genomics. The presentation I’ve shaped was intended to give a good overview of what needs to be learned by the newest generation of life scientists.
You don’t have to be an expert in code to actually benefit from better code and data know-how and good practices!

Following up the publication of the Study Group paper in PLoS Biology, I got invited to draft a publication in the Amsterdam Science Magazine.

Summary

After nearly a year of intense brainstorming, our story on building Study Groups is out in the open. Sarah and I act as community leads in Madison-Wisconsin (USA) and Amsterdam (Netherlands) at our respective Universities. Our communities of practice in scientific programming are affiliated to Mozilla Science Lab Study Groups foster and support Life Scientists lost under a data avalanche. Communities of practice in scientific programming help to break the impostor syndrome, network with other researchers engaged in programming and data analysis, break organisation silos that keep different fields and expertise separated, etc.

I’d like to organise code-review sessions in the near future with the aim of helping scientists to produce better more efficient code. Nonetheless, also having some documentation and testing would be nice!
I’ve compiled a few great resources and tips from the web in this blog post.
Hope it helps you if you’d like to organise similar things.
Cheers!

Yesterday, I organised a kick-start meeting to create a team of researchers that will lead the Study Group activities for the upcoming year.
With some experience and some further reading (see the other blog posts), I made a small agenda to convey the main information about the Study Group, its missions, values and what it takes to become a member.
I hope it helps others in organizing their own Study Group at their institution. Cheers!

Taken from the Mozilla Science Handbook:

From the Wikipedia article on sociocraty that helps to make a policy on decision making. The question is: what type of decision making policy do we want for a local community of practice in scientific programming. If we stick to the community values (see related post), then it should be a democratic and respectful decision making process. For now, there is no explicit structure which means that we need to implement one.

Still reading the great book from Michael Jacoby Brown “Building Powerful Community Organizations”. This post is on values that I want to convey through a to-be-founded Data Clinic at the University of Amsterdam.

I am reading this great book from Michael Jacoby Brown entitled “Building Powerful Community Organizations”. This post is a way for me to shape my ideas around a to-be-founded Data Clinic at the University of Amsterdam.

For some time now and after some discussion, I decided to start my own data analysis company and named it “biodata services”. The domain name www.biodataservices.nl is registered but I need to build the corresponding website and come up with a portfolio of the related activities!

Together with a list of scientists, I have recently written an article entitled “Building a local community of practice in scientific programming for Life Scientists”. This manuscript is under review for PLoS Biology at the time and already available on bioXriv here.

As I was willing to set-up a personal website for a while, I decided to give it a go following the nice example of Sarah Stevens and based on the Jekyll now template.