From fd3ff3c76f9e1195e122ff06791eb0ce38dd2533 Mon Sep 17 00:00:00 2001 From: Bet Figuerola <154223352+efigb@users.noreply.github.com> Date: Thu, 5 Dec 2024 15:28:10 +0100 Subject: [PATCH 1/6] Update BBglab_data_organization.md - changed page description and typos - added environmentally friendly practices from nextflow submit --- docs/BBGProtocols/BBglab_data_organization.md | 32 ++++++++++++++----- 1 file changed, 24 insertions(+), 8 deletions(-) diff --git a/docs/BBGProtocols/BBglab_data_organization.md b/docs/BBGProtocols/BBglab_data_organization.md index 83401322..f70b5b6a 100644 --- a/docs/BBGProtocols/BBglab_data_organization.md +++ b/docs/BBGProtocols/BBglab_data_organization.md @@ -1,15 +1,17 @@ -# BBGlab best practices on data organization +# BBGlab best practices -Here we present some best practices on how to organize data in projects in the **Cluster** and **Google Drive** to make your life easier and when day comes to be able to set up the **[BBGlab Exit protocol](https://drive.google.com/drive/folders/1veXAAucPqNQ2KIVFLyEJqPVjEeDcqsR-)**. +We all want the BBGlab to be a well-organized space where files or data — yours or a colleague's — are quick and easy to find. To help, we present some best practices on how to organize data in projects in the **Cluster** and **Google Drive** to make your life easier to save time and boost efficiency. With these practices, you will also be able to set up **[BBGlab Exit protocol](https://drive.google.com/file/d/1Z-jg7cLP7lAPZL0PC88pnozc_7gVF_2S/view?usp=drive_link)** handing things over when the time comes, making transitions easy and efficient for everyone. + +In addition, we've included practices focused on sustainability to help reduce our carbon footprint and promote an environmentally friendly workplace. ## Organizing the data ### Project Compilation -You MUST add the relevant information about your project to the ProjectCompilation excel for all the BBGlab members. It is the responsibility of all the people involved to keep it updated. +Essential information both for both finished and on going projects: -Essential information both for finished and for on going projects: - - Data + - Data: + remember it is **essential** that all your project data is updated and stored in [BBGlab datasets](https://docs.google.com/spreadsheets/d/10eVPI8X9dObmSdypmcID0DTxO1XW8h3AGHbm_IT0El8/edit?usp=sharing). Check how to do it in the BBGWiki **Datasets/Datasets_BBGLAB**. It is responsibility of all the users involved in the project to keep it updated! - Scripts - Environments - Notebooks @@ -19,9 +21,7 @@ Essential information both for finished and for on going projects: - Custom scripts - Environments in the cluster - Tools installed in your user in the cluster (some /bin folder somewhere) linked to source code -- Figures -- Abstracts, Slides, Posters, Manuscripts - + ### Google Drive You should have one directory per project shared (if necessary) with the people ivolved in the project. This directory MUST contain the following: @@ -90,6 +90,22 @@ Fill contact compilation sheet with contact details including: - Regular contacts +## Be environmentally friendly! + +Did you know it is estimated that the emission of a biology project (both wet and dry lab) has an estimated cost of 29 tCO2e/person? Or that a single analysis of RNA seq data of 10 million 100bp reads aligned to *P.falciparum* (13Gb, 1h 30) cost 240g CO2e? Also data storage has an environmental impact: a data center uses as much water as three average-sized hospitals. So our work also leaves a carbon footprint that we should be aware of and try to reduce it as much as possible. What can we do? + + - Reduce electricity + - Turn off the screens when you are not in the lab. Also the mouse and the keyboard + - Lock the computer when it is necessary + - Turn off the light of the lab when you are the last one leaving + - Reduce the CO2 cost of your coding: you can estimate the CO2 footprint of your scripts or pipelines and make it efficientlier with many tools like: + - [nf-co2footprint](https://github.com/nextflow-io/nf-co2footprint) + - [CodeCarbon](https://codecarbon.io/) + - [carbontracker](https://github.com/lfwa/carbontracker) + - Check out more [here](https://github.com/GreenAlgorithms/GreenAlgorithms4HPC) + +If you want to learn more about this take a look to Loïc Lannealongue session [Towards environmentally sustainable computational science with Green Algorithms](https://summit.nextflow.io/2024/barcelona/agenda/10-30--towards-environmentally-sustainable-computational-science/) presented nextflow submit Barcelona2 024. + ## Reference - Elisabet Figuerola - Ferriol Calvet From a4c9966c5d4d23e1beaefab77d1e66a344e84c02 Mon Sep 17 00:00:00 2001 From: Bet Figuerola <154223352+efigb@users.noreply.github.com> Date: Thu, 5 Dec 2024 16:53:24 +0100 Subject: [PATCH 2/6] Update docs/BBGProtocols/BBglab_data_organization.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/BBGProtocols/BBglab_data_organization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/BBGProtocols/BBglab_data_organization.md b/docs/BBGProtocols/BBglab_data_organization.md index f70b5b6a..5f80e8ca 100644 --- a/docs/BBGProtocols/BBglab_data_organization.md +++ b/docs/BBGProtocols/BBglab_data_organization.md @@ -8,7 +8,7 @@ In addition, we've included practices focused on sustainability to help reduce o ### Project Compilation -Essential information both for both finished and on going projects: +Essential information for both finished and ongoing projects: - Data: remember it is **essential** that all your project data is updated and stored in [BBGlab datasets](https://docs.google.com/spreadsheets/d/10eVPI8X9dObmSdypmcID0DTxO1XW8h3AGHbm_IT0El8/edit?usp=sharing). Check how to do it in the BBGWiki **Datasets/Datasets_BBGLAB**. It is responsibility of all the users involved in the project to keep it updated! From ebc9af573936433c8f5accb5dbd6e095b9788599 Mon Sep 17 00:00:00 2001 From: Bet Figuerola <154223352+efigb@users.noreply.github.com> Date: Thu, 5 Dec 2024 16:53:39 +0100 Subject: [PATCH 3/6] Update docs/BBGProtocols/BBglab_data_organization.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/BBGProtocols/BBglab_data_organization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/BBGProtocols/BBglab_data_organization.md b/docs/BBGProtocols/BBglab_data_organization.md index 5f80e8ca..4a0f338a 100644 --- a/docs/BBGProtocols/BBglab_data_organization.md +++ b/docs/BBGProtocols/BBglab_data_organization.md @@ -1,6 +1,6 @@ # BBGlab best practices -We all want the BBGlab to be a well-organized space where files or data — yours or a colleague's — are quick and easy to find. To help, we present some best practices on how to organize data in projects in the **Cluster** and **Google Drive** to make your life easier to save time and boost efficiency. With these practices, you will also be able to set up **[BBGlab Exit protocol](https://drive.google.com/file/d/1Z-jg7cLP7lAPZL0PC88pnozc_7gVF_2S/view?usp=drive_link)** handing things over when the time comes, making transitions easy and efficient for everyone. +We all want the BBGlab to be a well-organized space where files or data — yours or a colleague's — are quick and easy to find. To help, we present some best practices on how to organize data in projects in the **Cluster** and **Google Drive** to save time and boost efficiency. With these practices, you will also be able to set up **[BBGlab Exit protocol](https://drive.google.com/file/d/1Z-jg7cLP7lAPZL0PC88pnozc_7gVF_2S/view?usp=drive_link)** handing things over when the time comes, making transitions easy and efficient for everyone. In addition, we've included practices focused on sustainability to help reduce our carbon footprint and promote an environmentally friendly workplace. From b3a53f04a38257f0fb8cc69c81e992ef0ccc6262 Mon Sep 17 00:00:00 2001 From: Bet Figuerola <154223352+efigb@users.noreply.github.com> Date: Thu, 5 Dec 2024 16:54:15 +0100 Subject: [PATCH 4/6] Update docs/BBGProtocols/BBglab_data_organization.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/BBGProtocols/BBglab_data_organization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/BBGProtocols/BBglab_data_organization.md b/docs/BBGProtocols/BBglab_data_organization.md index 4a0f338a..8577d389 100644 --- a/docs/BBGProtocols/BBglab_data_organization.md +++ b/docs/BBGProtocols/BBglab_data_organization.md @@ -11,7 +11,7 @@ In addition, we've included practices focused on sustainability to help reduce o Essential information for both finished and ongoing projects: - Data: - remember it is **essential** that all your project data is updated and stored in [BBGlab datasets](https://docs.google.com/spreadsheets/d/10eVPI8X9dObmSdypmcID0DTxO1XW8h3AGHbm_IT0El8/edit?usp=sharing). Check how to do it in the BBGWiki **Datasets/Datasets_BBGLAB**. It is responsibility of all the users involved in the project to keep it updated! + remember it is **essential** that all your project data is updated and stored in [BBGlab datasets](https://docs.google.com/spreadsheets/d/10eVPI8X9dObmSdypmcID0DTxO1XW8h3AGHbm_IT0El8/edit?usp=sharing). Check how to do it in the BBGWiki **Datasets/Datasets_BBGLAB**. It is the responsibility of all the users involved in the project to keep it updated! - Scripts - Environments - Notebooks From 210265852afe34a46a043b8af2996865a6f865cb Mon Sep 17 00:00:00 2001 From: Bet Figuerola <154223352+efigb@users.noreply.github.com> Date: Thu, 5 Dec 2024 16:54:30 +0100 Subject: [PATCH 5/6] Update docs/BBGProtocols/BBglab_data_organization.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/BBGProtocols/BBglab_data_organization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/BBGProtocols/BBglab_data_organization.md b/docs/BBGProtocols/BBglab_data_organization.md index 8577d389..0d75e887 100644 --- a/docs/BBGProtocols/BBglab_data_organization.md +++ b/docs/BBGProtocols/BBglab_data_organization.md @@ -104,7 +104,7 @@ Did you know it is estimated that the emission of a biology project (both wet an - [carbontracker](https://github.com/lfwa/carbontracker) - Check out more [here](https://github.com/GreenAlgorithms/GreenAlgorithms4HPC) -If you want to learn more about this take a look to Loïc Lannealongue session [Towards environmentally sustainable computational science with Green Algorithms](https://summit.nextflow.io/2024/barcelona/agenda/10-30--towards-environmentally-sustainable-computational-science/) presented nextflow submit Barcelona2 024. +If you want to learn more about this take a look at Loïc Lannealongue session [Towards environmentally sustainable computational science with Green Algorithms](https://summit.nextflow.io/2024/barcelona/agenda/10-30--towards-environmentally-sustainable-computational-science/) presented nextflow submit Barcelona2 024. ## Reference - Elisabet Figuerola From d3b64b42db38af1673cb7523d6c01dc464b6b486 Mon Sep 17 00:00:00 2001 From: Bet Figuerola <154223352+efigb@users.noreply.github.com> Date: Thu, 5 Dec 2024 16:55:44 +0100 Subject: [PATCH 6/6] corrected typo --- docs/BBGProtocols/BBglab_data_organization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/BBGProtocols/BBglab_data_organization.md b/docs/BBGProtocols/BBglab_data_organization.md index 0d75e887..22707479 100644 --- a/docs/BBGProtocols/BBglab_data_organization.md +++ b/docs/BBGProtocols/BBglab_data_organization.md @@ -104,7 +104,7 @@ Did you know it is estimated that the emission of a biology project (both wet an - [carbontracker](https://github.com/lfwa/carbontracker) - Check out more [here](https://github.com/GreenAlgorithms/GreenAlgorithms4HPC) -If you want to learn more about this take a look at Loïc Lannealongue session [Towards environmentally sustainable computational science with Green Algorithms](https://summit.nextflow.io/2024/barcelona/agenda/10-30--towards-environmentally-sustainable-computational-science/) presented nextflow submit Barcelona2 024. +If you want to learn more about this take a look at Loïc Lannealongue session [Towards environmentally sustainable computational science with Green Algorithms](https://summit.nextflow.io/2024/barcelona/agenda/10-30--towards-environmentally-sustainable-computational-science/) presented nextflow submit Barcelona 2024. ## Reference - Elisabet Figuerola