Sharing. Connecting. Empowering
Find all the information about our community and projects at https://open-life-science.github.io.
First and foremost, Welcome! π Willkommen! π Bienvenue! π ΰ€Έΰ₯ΰ€Έΰ₯ΰ€΅ΰ€Ύΰ€ΰ€€ (Suswagat)πππ
This document (the README
file) is a hub to give you some information about the
project. Jump straight to one of the sections below, or just scroll down to find
out more.
We are working to create a mentoring program for individuals interested in becoming ambassadors for Open Science practice, training and education in their communities.
Our outcome is to support early stage researchers and young leaders by sharing Open Science skills, connecting them to others in the community, and empowering them to become ambassadors for Open Science practice, training and education in their communities.
We are currently a team of 3 members who share a passion for Open Research and inclusiveness in Open Science.
As the graduates, mentors, and hosts of various Mozilla Open Leaders cohorts, we have gained expertise in the technical and culture track. Furthermore, we participate in a wide range of activities in different international communities of practice in the life sciences: ELIXIR (European bioinformatics network), Galaxy, The Carpentries, Software Sustainability Institute (SSI), Open Bioinformatics Foundation (OBF), and Mozilla.
You! In whatever way you can help.
We need expertise in open-science, training, mentoring, communication. We'd love your feedback along the way, and of course.
If you think you can help in any of the areas listed above (and we bet you can) or in any of the many areas that we haven't yet thought of (and here we're sure you can) then please check out our contributors' guidelines and our roadmap.
Please note that it's very important to us that we maintain a positive and supportive environment for everyone who wants to participate. When you join us we ask that you follow our code of conduct in all interactions both on and offline.
You need a ruby
environment (version >= 2.4). Either you have it installed and
you know how to install Bundler and
Jekyll and then run Jekyll, or you use
(mini-)conda, a package management system
that can install all these tools for you. You can install it by following the
instructions on this page: https://conda.io/docs/user-guide/install/index.html
In the sequel, we assume you use miniconda.
Open a terminal
Clone this GitHub repository:
$ git clone https://github.com/open-life-science/open-life-science.github.io.git
Navigate to the open-life-science.github.io/
folder with cd
Set up the conda environment:
$ make create-env
Install the project's dependencies:
$ make install
Start the website:
$ make serve
Open the website in your favorite browser at: http://127.0.0.1:4000/
To avoid dead or wrong links, run the link checkers:
$ make check-html
To create a new blog post:
Create a file in the folder _posts
with a file named following the pattern yyyy-mm-dd-name.md
Add some metadata on the top of the file
---
layout: post
title: <title of the post>
author: <github id of the author>
image: images/yyyy-mm-dd-name.jpg
---
Add content of the post in the file in Markdown
Add images in images/posts/
Add someone to the list of people:
_data/people.yaml
filefirst-name
(mandatory)last-name
(mandatory)twitter
email
website
gitter
orcid
affiliation
city
country
(mandatory)pronouns
expertise
bio
Add the person to their corresponding list to be visible on the website:
_data/ols-n-projects.yaml
_data/ols-n-metadata.yaml
_data/ols-n-metadata.yaml
_data/ols-n-schedule.yaml
Add many people in a row to _data/people.yaml
:
Create a CSV file with at least the following columns (named this way):
First name
Last name
Email
Github username
Twitter username
Website
ORCID
Affiliation
City
Country
Pronouns
Areas of expertise (1 element per line)
Bio
A form like this one can be used to generate such csv
Get a copy of the CSV file at the root of this folder
Activate the conda environment
$ source activate open-life-science-website
Or alternatively, get locally:
Run the script which extract information from the CSV file and add them to _data/people.yaml
$ python bin/prepare_website_data.py extractpeople -i <path to csv file>
_data/partners.yaml
file-
) following an alphabetical ordername
website
description
images/partners
folder_data/partners.yaml
using logo
tagThe schedule displayed in a cohort page is automatically generated from a file _data/ols-n-schedule.yaml
.
In this file, for each week, it is listed the timeframe and the different calls planned. For each call, several information are given:
type
: Mentor-Mentee
, Cohort
, Mentors
or Coworking
duration
in mintitle
date
in the format Month Day, Year
time
in the format '14:00' and for Berlin timecalendar-event
: link to calendar eventagenda
: tldrnotes
: link to notesrecording
: link to recordingcontent
with details of the content written in Markdownbefore
with tasks to do before as a list written in Markdownafter
with tasks to do after as a list written in Markdownresources
: list of useful resources with for each of them:
type
: slides
, document
, or external-link
title
speaker
: username in _data/people.yaml
, if slideslink
Create a spreadsheet or CSV with columns:
Week
Start Date
Start Time
End Date
Duration
Title
Type
Learning objectives
Slides
Confirmed speaker
Note link
Recording
Hosts
Facilitators
Before
After
Adapt the script in bin/update_schedule.sh
with cohort id and link to CSV export of the spreadsheet
In metadata file for cohort, experts and possible mentors can be ordered by expertise area to be display in cohort page given these areas.
To order them:
Activate the conda environment
$ source activate open-life-science-website
Or alternatively, get locally:
Run the script which sort expertise and save information in metadata file
$ python bin/prepare_website_data.py sortexpertises -c <cohort id>
Create a CSV file with for each project the following information
Title
Mentor 1
Authors
Project-description
Comment regarding review
(with rejected
if needed)Keywords
Create a CSV file with participant information (similar as the one needed to add new people) with an extra column with project name
Activate the conda environment
$ source activate open-life-science-website
Or alternatively, get locally:
Run the script which extract project information from a CSV file and add them in project file
$ python bin/prepare_website_data.py addprojects \
-c <cohort id> \
-p <path to csv file with projects> \
-i <path to csv file with participants> \
-l <path to log file>
Create CSV file with
Week
Type
Optional
Subject
Start Date
Start Time
End Date
Duration
End Time
All Day Event
Note link
Description
Add events to Google calendar
Activate the conda environment
$ source activate open-life-science-website
Or alternatively, get locally:
Run the script which create new cohort files
$ python bin/prepare_website_data.py createcohort \
-c <cohort id> \
Update _config.yml
file to add new cohort in collection