On cats, farts and parrots.
I was invited to contribute to a seminar/discussion on AI, and using language models in research. These are the notes I prepared my short presentation. I am ...
Posts by Tags
AI
Bioconductor
Notes on software licenses
This post was motivated by the preparation of a the CytoPipeline package and the following question about software licenses. The CytoPipeline package is deve...
Notes on the CZI workshop on single cell proteomics and metabolomics
Here’s a summary of my recent short intro talk for the recent virtual CZI workshop on single cell proteomics and metabolomics, 8 April 2022.
New feature: annotated chromatograms
Today, I’m going to introduce a recent feature from the Spectra package, namely annotated chromatograms. I’ll start by showing the result and them explain ho...
May Institue keynote talk: Reproducible mass spectrometry-based research
These are my notes for my talk at the 2021 edition of the May Institute in Computation and statistics for mass spectrometry and proteomics.
Standardised and reproducible analysis of mass spectrometry-based single-cell proteomics data
We are excited to anounce the official release of the scp package. scp has been accepted in Bioconductor and published as its first stable release (version 1...
MSnbase contributors 2010 - 2020
I wrote the first MSnbase contributions post on the 27 November 2016 (udpated on the 4 January 2018), exactly 1247 day (3 years and 5 months) ago. It is time...
MSnbase contributors 2010 - 2016 2017
MSnbase (or here on GitHub) (Gatto and Lilley, 2010) is one of my main software projects. I started working on the package when I moved to Cambridge in 2010....
CBIO
CBIO’s internal communication goes open source
I have been using slack for a rather long time as a discussion platform for the lab, even before moving to Belgium. Based on the access log, I set up the lab...
CBIO’s EuroBioc2023 posters and talks
Long overdue now, but here are the CBIO lab’s contributions to the EuroBioc2023 conference that was organised on Ghent, on the 20 - 22 September 2023.
CPU
MSnbase contributors 2010 - 2016 2017
MSnbase (or here on GitHub) (Gatto and Lilley, 2010) is one of my main software projects. I started working on the package when I moved to Cambridge in 2010....
CCP LOPIT hackathon
Introduction
Cambridge
Supporting those that support Open Research
The Office of Scholarly Communication (OSC) is the main structure that focuses on all matters related to open research at the University of Cambridge. It sta...
Reproducible research - What should our goals be?
On Friday, I’ll be at the Reproducible Research workshop at the CRUK Cambridge Institute. I’ll be participating in a group discussing What should our goals b...
Open data info session
Earlier today, I attended an information session about Open Data presented by Marta Teperek from the Research data management team (@CamOpenData) at the Univ...
ChatGPT
On cats, farts and parrots.
I was invited to contribute to a seminar/discussion on AI, and using language models in research. These are the notes I prepared my short presentation. I am ...
ECR
HUPO ECR Online Panel Discussion - Getting recognised for your work
The HUPO Early Career Researcher (ECR) committee has organised a discussion panel on Getting recognised for your work and have asked me to participate - than...
How to Manage Data: Data Stewardship and FAIR Skills
In this interactive talk at the Hong Kong University of Science and Technology Research Data Management Symposium 2021, Laurent Gatto and Marta Teperek will ...
Open and reproducible management and dissemination of knowledge
This post is part of my application for the Circle U chair at the UCLouvain. The seven partners of Circle U set up a chair programme to ensure strong and sus...
Becoming a better scientist with open and reproducible research (2)
This is an modified version of the Becoming a better scientist with open and reproducible research talk that I gave at TU Delft in May 2019. This version was...
Becoming a better scientist with open and reproducible research
This blog post summarises the notes for my talk at the Are you ready for publishing reproducible research? meeting at the TU Delft on the 16 May 2019. The sl...
I won’t be Bullied Into Bad Science!
This is the content of my talk at OpenConCam, the OpenCon satellite meeting in Cambridge, presented on the 16 November 2017. The slides are available here.
An early career researcher’s view on modern and open scholarship
This post constitutes my talk at the OPEN SCIENCE IN PRACTICE 2017 summer school in Lausanne, on the 25 September 2017. The slides used during the presentati...
Bad publishing and bullied into bad science.
The recent long read about scientific publishing in the Guardian is fantastic. It depicts a very telling story of the research publishing landscape.
Supporting those that support Open Research
The Office of Scholarly Communication (OSC) is the main structure that focuses on all matters related to open research at the University of Cambridge. It sta...
Elsevier
Why Software and data papers are a bad solution to a real problem
I am unhappy and concerned with data/software papers: it’s is a bad answer to a real problem and we end up recapitulating the perverse incentives in academic...
MSnbase
MSnbase contributors 2010 - 2020
I wrote the first MSnbase contributions post on the 27 November 2016 (udpated on the 4 January 2018), exactly 1247 day (3 years and 5 months) ago. It is time...
MSnbase contributors 2010 - 2016 2017
MSnbase (or here on GitHub) (Gatto and Lilley, 2010) is one of my main software projects. I started working on the package when I moved to Cambridge in 2010....
OSC
Engaging Researchers in Good Data Management
Last months, I participated in the Engaging Researchers in Good Data Management meeting organised by the Office of Scholarly Communication, SPARC and Jisc (d...
Open Research Project
Exploring and sharing spatial proteomics data
I am very happy to be involved in the Open Research Project project, jointly organised and managed by the Wellcome Trust and the University of Cambridge’s Of...
Open Research Project, first thoughts
I am proud to be one of the participants in the Wellcome Trust Open Research Project (and here). The call was initially opened in December 2016 and was pitch...
OpenCon
I won’t be Bullied Into Bad Science!
This is the content of my talk at OpenConCam, the OpenCon satellite meeting in Cambridge, presented on the 16 November 2017. The slides are available here.
OpenConCam
I won’t be Bullied Into Bad Science!
This is the content of my talk at OpenConCam, the OpenCon satellite meeting in Cambridge, presented on the 16 November 2017. The slides are available here.
R
The Grid poster, in R
The MuseeL is the UCLouvain University museum in Louvain-la-Neuve. Highly recommended. It’s located to the lively place des sciences, in a nice brutalist sty...
Notes on software licenses
This post was motivated by the preparation of a the CytoPipeline package and the following question about software licenses. The CytoPipeline package is deve...
Notes on the CZI workshop on single cell proteomics and metabolomics
Here’s a summary of my recent short intro talk for the recent virtual CZI workshop on single cell proteomics and metabolomics, 8 April 2022.
New feature: annotated chromatograms
Today, I’m going to introduce a recent feature from the Spectra package, namely annotated chromatograms. I’ll start by showing the result and them explain ho...
How to succeed in my exam
This short post describes how to succeed and how to fail in answering a typical exam question in one of my bachelor courses. I even believe it is applicable ...
May Institue keynote talk: Reproducible mass spectrometry-based research
These are my notes for my talk at the 2021 edition of the May Institute in Computation and statistics for mass spectrometry and proteomics.
Standardised and reproducible analysis of mass spectrometry-based single-cell proteomics data
We are excited to anounce the official release of the scp package. scp has been accepted in Bioconductor and published as its first stable release (version 1...
MSnbase contributors 2010 - 2020
I wrote the first MSnbase contributions post on the 27 November 2016 (udpated on the 4 January 2018), exactly 1247 day (3 years and 5 months) ago. It is time...
MSnbase contributors 2010 - 2016 2017
MSnbase (or here on GitHub) (Gatto and Lilley, 2010) is one of my main software projects. I started working on the package when I moved to Cambridge in 2010....
The Fibonacci Sequence
Here’s another post inspired by some python code, this time about the Fibonacci sequence by Stuart Mumford.
CCP LOPIT hackathon
Introduction
The curse of dimensionality
Introduction
Running
Tribute to my first running watch
I have recently acquired a new running watch and wanted to give a little tribute to my TomTom runner watch that has accompanied my for just over 6 years and ...
These shoes are made for running
I’ve recently reached my 6 years running anniversary. My first recorded run was on the 10 February 2016, a decent 5 km run, starting from the wonderful Centr...
Spectra
New feature: annotated chromatograms
Today, I’m going to introduce a recent feature from the Spectra package, namely annotated chromatograms. I’ll start by showing the result and them explain ho...
UCLouvain
On cats, farts and parrots.
I was invited to contribute to a seminar/discussion on AI, and using language models in research. These are the notes I prepared my short presentation. I am ...
Podcasts du LLL: Et si on oubliait les notes?
Deuxième billet en français référençant un podcast du Louvain Learning Lab (le premier est ici). Cette fois, je fais un peu d’auto-promotion:
The Grid poster, in R
The MuseeL is the UCLouvain University museum in Louvain-la-Neuve. Highly recommended. It’s located to the lively place des sciences, in a nice brutalist sty...
Podcasts du LLL: repensons l’évaluation
Une fois n’est pas coutume, un billet en français, pour attirer votre attention sur les podcasts du LLL. Le LLL, ou Louvain Learning Lab accompagne tous les ...
Notes on interview questions
When it comes to interviews, I find it an extremely important to prepare a set of questions to identify what the overall message to pass across should be. An...
Using Lego as a metaphor to explain what I do
Below is a description of my research (and computational biology/bioinformatics in general) for non-scientists. It is a first attempt to the For beginners in...
Wellcome Trust
Exploring and sharing spatial proteomics data
I am very happy to be involved in the Open Research Project project, jointly organised and managed by the Wellcome Trust and the University of Cambridge’s Of...
Open Research Project, first thoughts
I am proud to be one of the participants in the Wellcome Trust Open Research Project (and here). The call was initially opened in December 2016 and was pitch...
academia
Notes on interview questions
When it comes to interviews, I find it an extremely important to prepare a set of questions to identify what the overall message to pass across should be. An...
Authorship, trust and open science
The publish or perish crisis has led to a situation where, quite understandably, being named on a paper is more important than the actual contribution. As a ...
analysis
Standardised and reproducible analysis of mass spectrometry-based single-cell proteomics data
We are excited to anounce the official release of the scp package. scp has been accepted in Bioconductor and published as its first stable release (version 1...
Some brief advice on data analysis
Following up from the Quantitative Proteomics and Data Analysis course, where in animated a discussion table about Inspection, visualisation and analysis of ...
children
Programming with pen and paper
Computer science is no more about computers than astronomy is about telescopes.
circle u
Open and reproducible management and dissemination of knowledge
This post is part of my application for the Circle U chair at the UCLouvain. The seven partners of Circle U set up a chair programme to ensure strong and sus...
communication
HUPO ECR Online Panel Discussion - Getting recognised for your work
The HUPO Early Career Researcher (ECR) committee has organised a discussion panel on Getting recognised for your work and have asked me to participate - than...
CBIO’s internal communication goes open source
I have been using slack for a rather long time as a discussion platform for the lab, even before moving to Belgium. Based on the access log, I set up the lab...
conference
CBIO’s EuroBioc2023 posters and talks
Long overdue now, but here are the CBIO lab’s contributions to the EuroBioc2023 conference that was organised on Ghent, on the 20 - 22 September 2023.
data
Engaging Researchers in Good Data Management
Last months, I participated in the Engaging Researchers in Good Data Management meeting organised by the Office of Scholarly Communication, SPARC and Jisc (d...
Research outputs management plans
During the talk about early career researchers’ view on modern and open scholarship I presented at the Research Data Management Forum 2017 in London, I descr...
Some brief advice on data analysis
Following up from the Quantitative Proteomics and Data Analysis course, where in animated a discussion table about Inspection, visualisation and analysis of ...
data champion
Engaging Researchers in Good Data Management
Last months, I participated in the Engaging Researchers in Good Data Management meeting organised by the Office of Scholarly Communication, SPARC and Jisc (d...
data champions
September data champions meeting
The Data Champions Initiative was set up as a way to promote best practice in terms of data management within the University departments and institutes, and ...
data management
How to Manage Data: Data Stewardship and FAIR Skills
In this interactive talk at the Hong Kong University of Science and Technology Research Data Management Symposium 2021, Laurent Gatto and Marta Teperek will ...
education
Podcasts du LLL: Et si on oubliait les notes?
Deuxième billet en français référençant un podcast du Louvain Learning Lab (le premier est ici). Cette fois, je fais un peu d’auto-promotion:
Podcasts du LLL: repensons l’évaluation
Une fois n’est pas coutume, un billet en français, pour attirer votre attention sur les podcasts du LLL. Le LLL, ou Louvain Learning Lab accompagne tous les ...
First ungrading assessment
Here’s the initial assessment of the new ungrading and feedback pedagogy that the TAs and myself have implemented this academic year (2022-2023). In a nutshe...
Ungrading my teaching
I have been extremely lucky to participate in a Carpentries instructor training as an early career researcher. By then, I had only taught a few workshops, an...
How to succeed in my exam
This short post describes how to succeed and how to fail in answering a typical exam question in one of my bachelor courses. I even believe it is applicable ...
Programming with pen and paper
Computer science is no more about computers than astronomy is about telescopes.
The steep learning curve
TL;DR The bloody steep learning curve is just a silly excuse and will only result in keeping [computer|programming|stats|…] literacy low in life sciences. St...
git
A gentle introduction to git and Github
Git is a command line-based distributed version control system. Version control system means that its goal is to track and record every change in a set of te...
Branch specific gitignores for Bioconductor package documentation
For more background on this post, see this thread on the Bioc-devel mailing list. The short story is that I use Hadley Wickham pkgdown package to build a web...
Git Svn
From my old Git(hub) notes…
interview
Notes on interview questions
When it comes to interviews, I find it an extremely important to prepare a set of questions to identify what the overall message to pass across should be. An...
job
Open position in the CBIO lab: spatial proteomics and PTMs
A position for a PhD student (4 years) or a research assistant (1 year contracts, renewable) is open in the CBIO lab focusing on protein sub-cellular localis...
Open position in the CBIO lab: single-cell proteomics
A fully-funded position for a PhD student (4 years) or a post-doctoral researcher (2 - 3 years, depending on experience) is open in the Computational Biology...
Open positions in the CBIO lab
There are a couple of opportunities to join the CBIO lab in 2022.
machine learning
The curse of dimensionality
Introduction
open access
Supporting those that support Open Research
The Office of Scholarly Communication (OSC) is the main structure that focuses on all matters related to open research at the University of Cambridge. It sta...
Why Software and data papers are a bad solution to a real problem
I am unhappy and concerned with data/software papers: it’s is a bad answer to a real problem and we end up recapitulating the perverse incentives in academic...
Authorship, trust and open science
The publish or perish crisis has led to a situation where, quite understandably, being named on a paper is more important than the actual contribution. As a ...
open data
Supporting those that support Open Research
The Office of Scholarly Communication (OSC) is the main structure that focuses on all matters related to open research at the University of Cambridge. It sta...
Research outputs management plans
During the talk about early career researchers’ view on modern and open scholarship I presented at the Research Data Management Forum 2017 in London, I descr...
How to get the most out of modern peer-review
Today, I participated in the How to get the most out of modern peer-review event organised by the Office of Scholarly Communication. Here’s a short summary a...
Why Software and data papers are a bad solution to a real problem
I am unhappy and concerned with data/software papers: it’s is a bad answer to a real problem and we end up recapitulating the perverse incentives in academic...
Authorship, trust and open science
The publish or perish crisis has led to a situation where, quite understandably, being named on a paper is more important than the actual contribution. As a ...
Open data info session
Earlier today, I attended an information session about Open Data presented by Marta Teperek from the Research data management team (@CamOpenData) at the Univ...
open research
One-minute introduction
Every now and then, there’s a situation where I need to briefly introduce myself, academically. This can be with or without any visual support (i.e a slide)....
How to Manage Data: Data Stewardship and FAIR Skills
In this interactive talk at the Hong Kong University of Science and Technology Research Data Management Symposium 2021, Laurent Gatto and Marta Teperek will ...
Open and reproducible management and dissemination of knowledge
This post is part of my application for the Circle U chair at the UCLouvain. The seven partners of Circle U set up a chair programme to ensure strong and sus...
May Institue keynote talk: Reproducible mass spectrometry-based research
These are my notes for my talk at the 2021 edition of the May Institute in Computation and statistics for mass spectrometry and proteomics.
Becoming a better scientist with open and reproducible research (2)
This is an modified version of the Becoming a better scientist with open and reproducible research talk that I gave at TU Delft in May 2019. This version was...
Standardised and reproducible analysis of mass spectrometry-based single-cell proteomics data
We are excited to anounce the official release of the scp package. scp has been accepted in Bioconductor and published as its first stable release (version 1...
So you want credit for your peer reviews?
Of course, it is only fair to get credit for the time and efforts researchers invest in reviewing their peers’ work. Especially so for early career researche...
Becoming a better scientist with open and reproducible research
This blog post summarises the notes for my talk at the Are you ready for publishing reproducible research? meeting at the TU Delft on the 16 May 2019. The sl...
A discussion about Open Access
Last week, Richard Poynder (@RickyPo on Twitter) organised an informal get together around open access (OA), that was attended by researchers, publishers and...
I won’t be Bullied Into Bad Science!
This is the content of my talk at OpenConCam, the OpenCon satellite meeting in Cambridge, presented on the 16 November 2017. The slides are available here.
An early career researcher’s view on modern and open scholarship
This post constitutes my talk at the OPEN SCIENCE IN PRACTICE 2017 summer school in Lausanne, on the 25 September 2017. The slides used during the presentati...
September data champions meeting
The Data Champions Initiative was set up as a way to promote best practice in terms of data management within the University departments and institutes, and ...
Peer review week: Panel discussion at Cambidge University Press
On the 17 August 2017, I participated in a panel discussion about peer review organised by Cambridge University Press (CUP). This post summarises some of the...
Bad publishing and bullied into bad science.
The recent long read about scientific publishing in the Guardian is fantastic. It depicts a very telling story of the research publishing landscape.
Supporting those that support Open Research
The Office of Scholarly Communication (OSC) is the main structure that focuses on all matters related to open research at the University of Cambridge. It sta...
Research outputs management plans
During the talk about early career researchers’ view on modern and open scholarship I presented at the Research Data Management Forum 2017 in London, I descr...
Open science and open science
A recent discussion on twitter about Open Sciences made me think about how Open Science can be intimidating, alienating and unwelcoming at times.
Exploring and sharing spatial proteomics data
I am very happy to be involved in the Open Research Project project, jointly organised and managed by the Wellcome Trust and the University of Cambridge’s Of...
How to get the most out of modern peer-review
Today, I participated in the How to get the most out of modern peer-review event organised by the Office of Scholarly Communication. Here’s a short summary a...
Open Research Project, first thoughts
I am proud to be one of the participants in the Wellcome Trust Open Research Project (and here). The call was initially opened in December 2016 and was pitch...
Authorship, trust and open science
The publish or perish crisis has led to a situation where, quite understandably, being named on a paper is more important than the actual contribution. As a ...
open science
Open science and open science
A recent discussion on twitter about Open Sciences made me think about how Open Science can be intimidating, alienating and unwelcoming at times.
pRoloc
CCP LOPIT hackathon
Introduction
peer review
So you want credit for your peer reviews?
Of course, it is only fair to get credit for the time and efforts researchers invest in reviewing their peers’ work. Especially so for early career researche...
September data champions meeting
The Data Champions Initiative was set up as a way to promote best practice in terms of data management within the University departments and institutes, and ...
Peer review week: Panel discussion at Cambidge University Press
On the 17 August 2017, I participated in a panel discussion about peer review organised by Cambridge University Press (CUP). This post summarises some of the...
How to get the most out of modern peer-review
Today, I participated in the How to get the most out of modern peer-review event organised by the Office of Scholarly Communication. Here’s a short summary a...
pre-prints
Early feedback on ‘Preprints could promote confusion and distortion’
In this News & Comments published in Nature on the 24 July, Tom Sheldon claims that Preprints could promote confusion and distortion and the public disse...
predatory publishing
Why Software and data papers are a bad solution to a real problem
I am unhappy and concerned with data/software papers: it’s is a bad answer to a real problem and we end up recapitulating the perverse incentives in academic...
programming
Branch specific gitignores for Bioconductor package documentation
For more background on this post, see this thread on the Bioc-devel mailing list. The short story is that I use Hadley Wickham pkgdown package to build a web...
The Fibonacci Sequence
Here’s another post inspired by some python code, this time about the Fibonacci sequence by Stuart Mumford.
Programming with pen and paper
Computer science is no more about computers than astronomy is about telescopes.
The steep learning curve
TL;DR The bloody steep learning curve is just a silly excuse and will only result in keeping [computer|programming|stats|…] literacy low in life sciences. St...
Git Svn
From my old Git(hub) notes…
The curse of dimensionality
Introduction
proteomics
Installing and running MaxQuant on GNU/Linux
After a first analysis of 20 plasma samples, we wanted to compare the results of a single acquisition against a fractionation of the same samples over 7 frac...
Notes on the CZI workshop on single cell proteomics and metabolomics
Here’s a summary of my recent short intro talk for the recent virtual CZI workshop on single cell proteomics and metabolomics, 8 April 2022.
New feature: annotated chromatograms
Today, I’m going to introduce a recent feature from the Spectra package, namely annotated chromatograms. I’ll start by showing the result and them explain ho...
May Institue keynote talk: Reproducible mass spectrometry-based research
These are my notes for my talk at the 2021 edition of the May Institute in Computation and statistics for mass spectrometry and proteomics.
Standardised and reproducible analysis of mass spectrometry-based single-cell proteomics data
We are excited to anounce the official release of the scp package. scp has been accepted in Bioconductor and published as its first stable release (version 1...
Exploring and sharing spatial proteomics data
I am very happy to be involved in the Open Research Project project, jointly organised and managed by the Wellcome Trust and the University of Cambridge’s Of...
Some brief advice on data analysis
Following up from the Quantitative Proteomics and Data Analysis course, where in animated a discussion table about Inspection, visualisation and analysis of ...
CCP LOPIT hackathon
Introduction
python
The Fibonacci Sequence
Here’s another post inspired by some python code, this time about the Fibonacci sequence by Stuart Mumford.
The curse of dimensionality
Introduction
reproducible research
How to Manage Data: Data Stewardship and FAIR Skills
In this interactive talk at the Hong Kong University of Science and Technology Research Data Management Symposium 2021, Laurent Gatto and Marta Teperek will ...
Open and reproducible management and dissemination of knowledge
This post is part of my application for the Circle U chair at the UCLouvain. The seven partners of Circle U set up a chair programme to ensure strong and sus...
May Institue keynote talk: Reproducible mass spectrometry-based research
These are my notes for my talk at the 2021 edition of the May Institute in Computation and statistics for mass spectrometry and proteomics.
Becoming a better scientist with open and reproducible research (2)
This is an modified version of the Becoming a better scientist with open and reproducible research talk that I gave at TU Delft in May 2019. This version was...
Notes on remote/online teaching
My (first) notes about remote teaching.
Becoming a better scientist with open and reproducible research
This blog post summarises the notes for my talk at the Are you ready for publishing reproducible research? meeting at the TU Delft on the 16 May 2019. The sl...
Reproducible research - What should our goals be?
On Friday, I’ll be at the Reproducible Research workshop at the CRUK Cambridge Institute. I’ll be participating in a group discussing What should our goals b...
research data
Engaging Researchers in Good Data Management
Last months, I participated in the Engaging Researchers in Good Data Management meeting organised by the Office of Scholarly Communication, SPARC and Jisc (d...
science
One-minute introduction
Every now and then, there’s a situation where I need to briefly introduce myself, academically. This can be with or without any visual support (i.e a slide)....
Using Lego as a metaphor to explain what I do
Below is a description of my research (and computational biology/bioinformatics in general) for non-scientists. It is a first attempt to the For beginners in...
The steep learning curve
TL;DR The bloody steep learning curve is just a silly excuse and will only result in keeping [computer|programming|stats|…] literacy low in life sciences. St...
single cell
Notes on the CZI workshop on single cell proteomics and metabolomics
Here’s a summary of my recent short intro talk for the recent virtual CZI workshop on single cell proteomics and metabolomics, 8 April 2022.
Standardised and reproducible analysis of mass spectrometry-based single-cell proteomics data
We are excited to anounce the official release of the scp package. scp has been accepted in Bioconductor and published as its first stable release (version 1...
software
CBIO’s EuroBioc2023 posters and talks
Long overdue now, but here are the CBIO lab’s contributions to the EuroBioc2023 conference that was organised on Ghent, on the 20 - 22 September 2023.
One-minute introduction
Every now and then, there’s a situation where I need to briefly introduce myself, academically. This can be with or without any visual support (i.e a slide)....
Notes on software licenses
This post was motivated by the preparation of a the CytoPipeline package and the following question about software licenses. The CytoPipeline package is deve...
New feature: annotated chromatograms
Today, I’m going to introduce a recent feature from the Spectra package, namely annotated chromatograms. I’ll start by showing the result and them explain ho...
May Institue keynote talk: Reproducible mass spectrometry-based research
These are my notes for my talk at the 2021 edition of the May Institute in Computation and statistics for mass spectrometry and proteomics.
Research outputs management plans
During the talk about early career researchers’ view on modern and open scholarship I presented at the Research Data Management Forum 2017 in London, I descr...
Why Software and data papers are a bad solution to a real problem
I am unhappy and concerned with data/software papers: it’s is a bad answer to a real problem and we end up recapitulating the perverse incentives in academic...
spatial
Exploring and sharing spatial proteomics data
I am very happy to be involved in the Open Research Project project, jointly organised and managed by the Wellcome Trust and the University of Cambridge’s Of...
CCP LOPIT hackathon
Introduction
svn
Branch specific gitignores for Bioconductor package documentation
For more background on this post, see this thread on the Bioc-devel mailing list. The short story is that I use Hadley Wickham pkgdown package to build a web...
Git Svn
From my old Git(hub) notes…
talk
September data champions meeting
The Data Champions Initiative was set up as a way to promote best practice in terms of data management within the University departments and institutes, and ...
talks
CBIO’s EuroBioc2023 posters and talks
Long overdue now, but here are the CBIO lab’s contributions to the EuroBioc2023 conference that was organised on Ghent, on the 20 - 22 September 2023.
How to Manage Data: Data Stewardship and FAIR Skills
In this interactive talk at the Hong Kong University of Science and Technology Research Data Management Symposium 2021, Laurent Gatto and Marta Teperek will ...
May Institue keynote talk: Reproducible mass spectrometry-based research
These are my notes for my talk at the 2021 edition of the May Institute in Computation and statistics for mass spectrometry and proteomics.
Becoming a better scientist with open and reproducible research (2)
This is an modified version of the Becoming a better scientist with open and reproducible research talk that I gave at TU Delft in May 2019. This version was...
Becoming a better scientist with open and reproducible research
This blog post summarises the notes for my talk at the Are you ready for publishing reproducible research? meeting at the TU Delft on the 16 May 2019. The sl...
An early career researcher’s view on modern and open scholarship
This post constitutes my talk at the OPEN SCIENCE IN PRACTICE 2017 summer school in Lausanne, on the 25 September 2017. The slides used during the presentati...
teaching
Podcasts du LLL: Et si on oubliait les notes?
Deuxième billet en français référençant un podcast du Louvain Learning Lab (le premier est ici). Cette fois, je fais un peu d’auto-promotion:
Podcasts du LLL: repensons l’évaluation
Une fois n’est pas coutume, un billet en français, pour attirer votre attention sur les podcasts du LLL. Le LLL, ou Louvain Learning Lab accompagne tous les ...
First ungrading assessment
Here’s the initial assessment of the new ungrading and feedback pedagogy that the TAs and myself have implemented this academic year (2022-2023). In a nutshe...
Ungrading my teaching
I have been extremely lucky to participate in a Carpentries instructor training as an early career researcher. By then, I had only taught a few workshops, an...
How to succeed in my exam
This short post describes how to succeed and how to fail in answering a typical exam question in one of my bachelor courses. I even believe it is applicable ...
Notes on remote/online teaching
My (first) notes about remote teaching.
A gentle introduction to git and Github
Git is a command line-based distributed version control system. Version control system means that its goal is to track and record every change in a set of te...
Using Lego as a metaphor to explain what I do
Below is a description of my research (and computational biology/bioinformatics in general) for non-scientists. It is a first attempt to the For beginners in...
Some brief advice on data analysis
Following up from the Quantitative Proteomics and Data Analysis course, where in animated a discussion table about Inspection, visualisation and analysis of ...
Programming with pen and paper
Computer science is no more about computers than astronomy is about telescopes.