(Story originally published on Medium) MLFlow is a tool used to manage the development of Machine Learning models, from their development to release in production. It is also a great tool for managing bioinformatics analyses, making it easier to test parameters and options and reproduce results. However, in my opinion, not many Bioinformaticians are aware
Foundation Models for Bioinformatics – a Primer
(Original article published on Medium) Foundation models for biology are one of the most significant technological advances in bioinformatics in recent years. However, they are built on concepts that can be relatively unfamiliar to people in the field, as they are derived from other areas of AI. This article summarises what you need to know
Applicazioni di chatGPT e altri LLMs per la ricerca di farmaci
LLMs and foundation models are changing the way drug discovery is done – it’s still early days, but there is no denying it. However, when you talk about it with someone outside the field, they often have no idea what you are talking about. Some people have heard of chatGPT, but only a few have
Book Lovers’ day 2022
Yesterday it was Book Lovers’ day! Thanks to Brady Todd for reminding me. Here is a list of books I have read recently and recommend. – The Maverick by Ricardo Semler: this is a great classic on Leadership and on how to organize a company. It tells the story of Semco, a Brazilian company where all employees
a Bioinformatician in the Big Pharma
The last 18 months have been quite a radical career change for me. This is because I made the infamous move: leaving the Academia and starting working in the Industry. To be honest I am quite happy of the change. I’ve learned many things, discovered another way to do science, and possibly made some contributions. Moving from
Hacking Global Health London 2016
A few months ago I’ve participated in a Hackaton organized by Open Data Science on data from the Healthy Growth, Birth, Development knowledge integration (HBGDki) initiative by the Bill and Melinda Gates foundation. The aim of this initiative is to collect data on child growth and development from several sources, to study which factors influence child
Published a “Post Publication Review” on Publons
A while ago I posted in this blog an analysis on fitness genes, illustrating an use of the Bioconductor data packages and based on a recently published paper (Are fitness genes more conserved across species?). This week I have been contacted by the team of Publons and asked to paste the same analysis on their platform as a
Hiding cows in the genome (a.k.a. an introduction to bash programming)
Preparing the materials for a workshop on bash programming is very difficult, because you never know which level of skill to expect from the people attending it. Most of the times the class will be a mix of absolute beginners and expert Unix users, and it is not easy to prepare a presentation that will interest
Data Annotation Packages in BioConductor
Bioconductor does not only contain analysis packages, but also a good suite of data packages, frozen from the most important data sources for bioinformatics (e.g. EBI, NCBI, UCSC, etc..). These data packages are useful because because they allow to access certain biological relevant data quickly and without having to manually download them from the web. They
Interviewed by LabWorm for NCG
Our group has been interviewed by LabWorm regarding our recent publication on Network of Cancer Genes 5.0. I absolutely love the “artist impression” they made of our team: LabWorm is a collaborative platform for sharing tools and links related to bioinformatics. They have a very modern and interactive user interface, and they are very active