...
 
Commits (2)
......@@ -7,7 +7,8 @@ variables:
before_script:
- bundle install
- bundle exec just-the-docs rake search:init
- python check_links_include.py
- python --version
# - python check_links_include.py
- cat _timestamp_files.txt | xargs python add_timestamp.py
test:
......
[alexandrov-lab]: https://www.embl.de/research/units/scb/alexandrov/
[bio-it-blogs]: https://grp-bio-it.embl-community.io/blogs/
[bio-it-blogs-repo]: https://git.embl.de/grp-bio-it/blogs/
[bio-it-compute-info]: https://bio-it.embl.de/computing-resources/
[bio-it-courses]: https://bio-it.embl.de/upcoming-courses/
[bio-it-course-materials]: https://bio-it.embl.de/course-materials/
[bio-it-get-involved]: https://bio-it.embl.de/get-involved/
[bio-it-gitlab-pages]: https://bio-it.embl.de/gitlab-pages/
[bio-it-homepage]: https://bio-it.embl.de/
[bio-it-reports]: https://git.embl.de/grp-bio-it/bio-it-reports
......
why/background.md
what/course-metrics.md
what/reporting.md
what/resource-metrics.md
what/service-usage-demand.md
when/milestones.md
where/technical-needs.md
who/target-audience.md
about/background.md
coordination/strategy/course-metrics.md
coordination/strategy/reporting.md
coordination/strategy/resource-metrics.md
coordination/strategy/service-usage-demand.md
coordination/strategy/milestones.md
coordination/strategy/technical-needs.md
about/target-audience.md
---
title: About the Community
layout: page
permalink: /about/
has_children: true
nav_order: 1
---
In this section,
we provide an overview of the community and the goals of the Bio-IT Project.
This is a good place to start if you're new to EMBL and/or the community project.
We include a set of *community personas*:
(fictionalised) archetypes of the different people who make up our community,
and information on how engaging with the community might benefit them.
---
title: Project Background
layout: page
permalink: /why/background/
parent: Why
permalink: /about/background/
parent: About the Community
tags: ["strategy", "motivation"]
---
......@@ -28,7 +28,7 @@ biologists and bioinformaticians at the institute.
In its early stages,
the project built on the existing
[grassroots efforts of a group of computational staff]({{site.baseurl}}who/taskforce/)
[grassroots efforts of a group of computational staff]({{site.baseurl}}members/taskforce/)
who were already working collaboratively to establish a unified library of
Linux software tools available across the various different compute environments that existed at EMBL Heidelberg at the time.
......@@ -50,7 +50,7 @@ The community has benefitted from many other important developments in addition
## Project Coordination
Project strategy and activity is largely discussed and planned
by the [Bio-IT Taskforce]({{site.baseurl}}who/taskforce/).
by the [Bio-IT Taskforce]({{site.baseurl}}members/taskforce/).
Within this group, the following people are responsible
for coordination of project activity:
......
---
title: Bio-IT Mission
layout: page
permalink: /why/mission/
parent: Why
permalink: /about/mission/
parent: About the Community
tags: ["strategy", "motivation"]
---
......
......@@ -2,8 +2,8 @@
title: Community Personas
description: Profiles of the different types of persona that make up the Bio-IT community.
layout: page
permalink: /why/personas/
parent: Why
permalink: /about/personas/
parent: About the Community
tags: ["motivation"]
---
......
---
title: "Computational Activity at EMBL Heidelberg"
layout: page
permalink: /who/target-audience/
parent: Who
permalink: /about/target-audience/
parent: About
tags: ["metrics", "surveys"]
---
......@@ -14,7 +14,7 @@ asking them to estimate the proportion of research activity
that is primarily computational, within their group.
In more recent surveys, additional questions have been asked
in an attempt to assess the impact of the various support activities
(e.g. see [Usage & Demand of Bio-IT Services & Resources]({{site.baseurl}}what/service-metrics/)).
(e.g. see [Usage & Demand of Bio-IT Services & Resources]({{site.baseurl}}coordination/strategy/service-metrics/)).
Project coordinators use the information collected
to try to understand the needs of the community,
......
---
title: Checklists
layout: page
permalink: /checklists/
has_children: true
nav_order: 4
---
This is a collection of checklists and guides
used within the Bio-IT community.
These lists are useful when organising/running events
and taking care of various administrative and promotional tasks.
TODO: beer sessions; seminars; lunches
---
title: "HOWTO: Barbecue @EMBL"
layout: page
permalink: /how/bbq/
parent: How
permalink: /checklists/bbq/
parent: Checklists
tags: ["in-person", "social", "casual", "community building", "acknowledgment", "events"]
---
......
---
title: "HOWTO: External Training"
layout: page
permalink: /how/course-external/
parent: How
permalink: /checklists/course-external/
parent: Checklists
tags: ["in-person", "training", "events"]
---
This list is intended to supplement
[the checklist for internal training events]({{site.baseurl}}how/course-internal/)
[the checklist for internal training events]({{site.baseurl}}checklists/course-internal/)
## Before the course
......
---
title: "HOWTO: CollaborationFest @EMBL"
layout: page
permalink: /how/cofest/
parent: How
permalink: /checklists/cofest/
parent: Checklists
tags: ["in-person", "online", "social", "collaboration", "community building", "training", "events"]
---
......
---
title: "HOWTO: Internal Training"
layout: page
permalink: /how/course-internal/
parent: How
permalink: /checklists/course-internal/
parent: Checklists
tags: ["in-person", "online", "training", "events"]
---
......@@ -44,7 +44,7 @@ tags: ["in-person", "online", "training", "events"]
## See also
- Organising an external course? See the additional items in the [External Courses checklist]({{site.baseurl}}how/course-external)
- Providing a live stream connection to your course? See the additional items in the [Teaching via Live Stream checklist]({{site.baseurl}}how/online-teaching/)
- Organising an external course? See the additional items in the [External Courses checklist]({{site.baseurl}}checklists/course-external)
- Providing a live stream connection to your course? See the additional items in the [Teaching via Live Stream checklist]({{site.baseurl}}checklists/online-teaching/)
{% include links.md %}
---
title: "HOWTO: Online Meeting"
layout: page
permalink: /how/online-meeting/
parent: How
permalink: /checklists/online-meeting/
parent: Checklists
tags: ["online", "events"]
---
......
---
title: "HOWTO: Teaching via Live Stream"
layout: page
permalink: /how/online-teaching/
parent: How
permalink: /checklists/online-teaching/
parent: Checklists
tags: ["online", "training"]
---
This list is intended to supplement
the checklists
[for internal training events]({{site.baseurl}}checklists/course-internal/)
and [external training events]({{site.baseurl}}checklists/course-external/)
## Before the course
- [ ] Make sure that venue has video conferencing infrastructure
......
---
title: "HOWTO: Order Stickers"
layout: page
permalink: /how/stickers/
parent: How
permalink: /checklists/stickers/
parent: Checklists
tags: ["marketing", "outreach", "community building", "acknowledgment"]
---
......
---
title: "HOWTO: Bio-IT Taskforce Meeting"
layout: page
permalink: /how/taskforce-meeting/
parent: How
permalink: /checklists/taskforce-meeting/
parent: Checklists
tags: ["in-person", "events", "community building", "strategy"]
---
......
---
title: For Community Coordinators
layout: page
permalink: /coordination/
has_children: true
nav_order: 2
---
These pages are designed for community coordinators,
documenting various administrative processes,
important resources for project management,
providing an archive of project activity,
and listing events and dates important in the project lifecycle.
TODO: add more links to [Useful Links](useful-links/).
---
title: Community Platforms
layout: page
permalink: /coordination/platforms/
parent: For Community Coordinators
has_children: true
nav_order: 2
---
{% include links.md %}
---
title: Bio-IT Wordpress Info
layout: page
permalink: where/bio-it-home/
parent: Where
permalink: coordination/platforms/bio-it-home/
parent: Community Platforms
tags: []
---
......@@ -17,7 +17,7 @@ and handles subscriptions to the Bio-IT and Centres mailing lists.
The front page of the site contains a table of links
to pages and other sites,
divided according to the [four objectives of the project]({{site.baseurl}}why/mission/):
divided according to the [four objectives of the project]({{site.baseurl}}about/mission/):
Training & Consulting;
Community Building;
Information Dissemination;
......
---
title: EMBL GitLab
layout: page
permalink: /where/gitlab/
parent: Where
permalink: /coordination/platforms/gitlab/
parent: Community Platforms
tags: []
---
......@@ -21,7 +21,7 @@ which
(like [GitHub][github])
provides a graphical interface to manage projects under version control,
has been
[increasingly popular]({{site.baseurl}}what/resource-metrics/)
[increasingly popular]({{site.baseurl}}coordination/strategy/resource-metrics/)
ever since.
## Mattermost
......@@ -85,7 +85,7 @@ are all hosted on virtual machines provided by EMBL IT Services.
Costs incurred for additional storage are covered by the Bio-IT budget.
The systems are managed by
the [EMBL Git Admins]({{site.baseurl}}who/git-admins/):
the [EMBL Git Admins]({{site.baseurl}}members/git-admins/):
volunteers from the community
who handle user accounts,
keep software up-to-date,
......
---
title: Community Processes
layout: page
permalink: /coordination/processes/
parent: For Community Coordinators
has_children: true
nav_order: 3
---
---
title: "HOWTO: Review Outreach & Travel Fellowship Applications"
layout: page
permalink: /how/fellowship-applications/
parent: How
tags: ["acknowledgment", "fellowship", "training", "outreach"]
permalink: /coordination/processes/fellowship-applications/
parent: Community Processes
tags: ["gratitude", "fellowship", "training", "outreach"]
---
Community members apply for the
......@@ -16,7 +16,7 @@ Each application should be reviewed according to the following criteria:
- Is there sufficient unused funding allocated to the Fellowship to cover the application?
- Has the applicant actively contributed to the Bio-IT Project in the last year?
- this could be via teaching, developing/maintaining a resource for the community, helping run an event, writing a blogpost, answering questions online, or anything else that's benefitted the community
- Is the activity for which they are requesting financial support relevant to [the mission]({{site.baseurl}}why/mission/) of the Bio-IT Project?
- Is the activity for which they are requesting financial support relevant to [the mission]({{site.baseurl}}about/mission/) of the Bio-IT Project?
- Will the activity for which they are requesting financial support benefit the applicant and the wider community?
- Has the applicant already received funding up to the annual limit for the year?
......
---
title: Strategy & Reporting
layout: page
permalink: /coordination/strategy/
parent: For Community Coordinators
has_children: true
nav_order: 1
---
Information on previous Bio-IT Project activity,
motivation and context for project strategy,
and details of when and how activity is reported.
{% include links.md %}
---
title: "Course History & Feedback"
layout: page
permalink: /what/course-metrics/
parent: What
permalink: /coordination/strategy/course-metrics/
parent: Strategy & Reporting
tags: ["metrics", "training", "reports"]
---
......@@ -12,7 +12,7 @@ The history of Bio-IT courses and workshops is listed in
[the `/grp-bio-it/bio-it-reports` repository][bio-it-reports]
(internal access only).
That file includes a summary of the feedback collected for each course.
For more about course feedback, see the page on [Reporting]({{site.baseurl}}what/reporting/)
For more about course feedback, see the page on [Reporting]({{site.baseurl}}coordination/strategy/reporting/)
TODO training infographic
......
---
title: Milestones
layout: page
permalink: /when/milestones/
parent: When
permalink: /coordination/strategy/milestones/
parent: Strategy & Reporting
tags: ['reporting', 'strategy']
---
......
---
title: Repeating Events
layout: page
permalink: /how/repeating-events/
parent: How
permalink: /coordination/strategy/repeating-events/
parent: Strategy & Reporting
tags: ["in-person", "online", "events"]
---
......@@ -29,7 +29,7 @@ A list of repeating events for the Bio-IT community.
- Taskforce Meetings
- bi-monthly, taking place at 14:00 on the first Wednesday of odd-number months
- see [Taskforce Meeting HOWTO]({{site.baseurl}}how/taskforce-meeting/) for details
- see [Taskforce Meeting HOWTO]({{site.baseurl}}checklists/taskforce-meeting/) for details
- Bio-IT lunch
- roughly monthly
- a lunch bringing together Bio-IT coordinators, bioinformatics/computational support staff, members of IT Services, and other major contributors to the Bio-IT Project
......
---
title: "Bio-IT Reporting"
layout: page
permalink: /what/reporting/
parent: What
permalink: /coordination/strategy/reporting/
parent: Strategy & Reporting
tags: ["metrics", "reports", "meetings"]
---
......@@ -13,7 +13,7 @@ tags: ["metrics", "reports", "meetings"]
### Taskforce Meeting Minutes
Notes from the bi-monthly meetings of the [Bio-IT Taskforce]({{site.baseurl}}who/taskforce/)
Notes from the bi-monthly meetings of the [Bio-IT Taskforce]({{site.baseurl}}members/taskforce/)
are stored in [the `grp-bio-it/taskforce-minutes` repository][taskforce-minutes]
(internal access only).
......@@ -55,7 +55,7 @@ measure and report the quality of our courses,
understand how we can improve our teaching and/or materials,
and plan new courses.
Feedback may be collected from other events,
such as [CollaborationFests]({{site.baseurl}}how/cofest/) or other events being run for the first time,
such as [CollaborationFests]({{site.baseurl}}checklists/cofest/) or other events being run for the first time,
where the organisers wish to gather
suggestions for improving the next incarnation,
information for reporting,
......
---
title: "Resource Usage Metrics"
layout: page
permalink: /what/resource-metrics/
parent: What
permalink: /coordination/strategy/resource-metrics/
parent: Strategy & Reporting
tags: ["metrics", "resources", "reports", "gitlab"]
---
......
---
title: "Usage & Demand of Bio-IT Services & Resources"
layout: page
permalink: /what/service-metrics/
parent: What
permalink: /coordination/strategy/service-metrics/
parent: Strategy & Reporting
tags: ["metrics", "reports"]
---
......
---
title: Technical Needs of the Community
layout: page
parent: Where
permalink: /where/technical-needs/
permalink: /coordination/strategy/technical-needs/
parent: Strategy & Reporting
tags: []
---
......@@ -14,7 +14,7 @@ We can describe the technical needs of the community in terms of:
In addition to these technical needs,
community members also require access to training to use these tools effectively.
See [this page]({{site.baseurl}}where/training-needs/) for more information on this topic.
See [this page]({{site.baseurl}}coordination/strategy/training-needs/) for more information on this topic.
* table of contents
{:toc}
......@@ -132,7 +132,7 @@ The library of modules is built according to a collection of
EasyBuild descriptions maintained by members of IT Services
and volunteers from the Bio-IT community
and deployed via the Continuous Integration system
associated with the [EMBL GitLab]({{site.baseurl}}where/gitlab/).
associated with the [EMBL GitLab]({{site.baseurl}}coordination/platforms/gitlab/).
As another way to reduce the difficulty of installing and running software,
Containers can be run with [Singularity][singularity] on the EMBL cluster,
......
---
title: Training Needs of the Community
layout: page
parent: Where
permalink: /where/training-needs/
permalink: /coordination/strategy/training-needs/
parent: Strategy & Reporting
tags: []
---
......@@ -34,7 +34,7 @@ The need for computational training falls into three categories:
- machine learning
- image processing/analysis
- workflow management
- additional specialised training is provided by the [EMBL Computational Centres]({{site.baseurl}}who/centres/) and several EMBL Core Facilities
- additional specialised training is provided by the [EMBL Computational Centres]({{site.baseurl}}members/centres/) and several EMBL Core Facilities
### Identifying New Training Topics
......
---
title: Useful Links
layout: page
permalink: /where/links/
parent: Where
permalink: /coordination/links/
parent: For Community Coordinators
nav_order: 4
---
* table of contents
......@@ -18,9 +19,9 @@ the configuration and maintenance of various Bio-IT resources.
- contains configurations and setup documentation for the internal GitLab system, Mattermost chat, and continuous integration server/runner
- [Community Documentation repository]({{site.aux_links["Source"]}})
- the source files for this site
- see [the page about GitLab Pages]({{site.baseurl}}where/gitlab/#gitlab-pages) for more information
- see [the page about GitLab Pages]({{site.baseurl}}coordination/platforms/gitlab/#gitlab-pages) for more information
- [Bio-IT Blogs repository][bio-it-blogs-repo]
- see [the page about GitLab Pages]({{site.baseurl}}where/gitlab-pages/) for more information
- see [the page about GitLab Pages]({{site.baseurl}}coordination/platforms/gitlab/#gitlab-pages) for more information
## External
......
---
title: How
layout: page
permalink: /how/
has_children: true
nav_order: 5
---
## Suggested content
- Programming
- content calendar
- meeting schedule
- etc
- Community guidelines
- Moderations procedures/escalation paths
- Best practices for community management
## Bio-IT content
- checklists
- course/workshop organisation DONE
- rearrange into before/during/after TODO
- event organisation
- beer sessions
- lunches
- hackathons WIP
- BBQ DONE
- meeting HOWTOs DONE
- calendar/schedule of repeating events DONE
- Taskforce meetings DONE
- lunches DONE
- beer sessions DONE
- BBQ DONE
- drop-in sessions DONE
- ordering stickers DONE
- Bio-IT Travel & Outreach Fellowship DONE
......@@ -15,7 +15,8 @@ community at the [European Molecular Biology Laboratory (EMBL)][embl-homepage],
These docs provide information and practical guides about the community, the project,
and its activities.
They were originally developed by [Toby Hodges][toby-homepage]
as part of the [CSCCE Community Engagement Fellows Program][cefp-homepage] 2019 (CEFP2019).
as part of the
[CSCCE Community Engagement Fellows Program][cefp-homepage] 2019 (CEFP2019).
If you have questions about these pages,
about our community,
......
---
title: For Community Members
layout: page
permalink: /members/
has_children: true
nav_order: 2
---
The [Bio-IT Portal][bio-it-homepage] is intended to provide
most information relevant to community members,
such as [course listings][bio-it-courses]
and [materials][bio-it-course-materials],
a [guide for newcomers][bio-it-newcomers-guide],
and details of
[compute resources available to community members][bio-it-compute-info].
That site also provides everything you need to know about how to
[__get involved with the Bio-IT community__][bio-it-get-involved].
Here we provide further information that may be interesting to community
members, about various important groups within the community,
and the way that Bio-IT training is organised and delivered.
---
title: EMBL Computational Centres
layout: page
permalink: /who/centres/
parent: Who
permalink: /members/centres/
parent: For Community Members
tags: []
---
......
---
title: EMBL Git Admins
layout: page
permalink: /who/git-admins/
parent: Who
permalink: /members/git-admins/
parent: For Community Members
tags: []
---
......
---
title: How we teach
layout: page
permalink: /members/how-we-teach/
parent: For Community Members
tags: []
---
---
title: Bio-IT Instructors
layout: page
permalink: /members/instructors/
parent: For Community Members
tags: []
---
---
title: Bio-IT Taskforce
layout: page
permalink: /who/taskforce/
parent: Who
permalink: /members/taskforce/
parent: For Community Members
tags: ["strategy", "gratitude"]
---
......@@ -16,7 +16,7 @@ research group leaders with an interest and/or remit for bioinformatics support,
and members of the IT Services group.
The Taskforce originally formed around the group whose grassroots activity,
establishing a common library of Linux software tools for EMBL systems,
[led to the foundation of the Bio-IT Project]({{site.baseurl}}why/background/):
[led to the foundation of the Bio-IT Project]({{site.baseurl}}about/background/):
Jean-Karim Hériché,
Venkata Satagopam,
and Frank Thommen.
......
---
title: What
layout: page
permalink: /what/
has_children: true
nav_order: 4
---
## Suggested content
- Funding distribution decisions
- Progress reports
- Metrics & evaluation
## Bio-IT content
- guide to reporting DONE
- SSMAC reports DONE
- writing Taskforce meeting minutes DONE
- course & event history files DONE
- course feedback summary
- GitLab + chat usage summary & link to gitlab-metrics repo DONE
- survey info on service usage/awareness
- latest version of summary slide/figure/infographic
---
title: When
layout: page
permalink: /when/
has_children: true
nav_order: 7
---
## Suggested content
- Community roadmap
- Funding cycles/other deadlines
- Publication plan
- Meeting calendar
- Lifecycle stage
## Bio-IT content
- fixed important events:
- next SCB review
- next 3-year survey
- next SCB unit seminar
- next "Thank You" BBQ
- list of repeating events DONE ([in HOW]({{site.baseurl}}how/repeating-events/))
- link to HOW section for organisation guidelines
---
title: Where
layout: page
permalink: /where/
has_children: true
nav_order: 6
---
## Suggested content
- Tools selection & community orientations
- clarification of the technical needs of the community
- Tools landscape
- specific tools in use by the community
- Platform specific information
- platform vendors, maintenance, integration, etc
## Bio-IT content
tools for the community
- list of (technical) needs of community WIP
- computing - cluster, software, RStudio Server, servers, training
- communication - chat, blog, networking events
- collaboration - GitLab
- GitLab, Mattermost DONE
- links to docs, git-admin repo
tools for community management
- Wordpress DONE
- links to docs, tutorials, key plugins, etc
- Blogs DONE
- link to docs, repo
- list of important links WIP
---
title: Who
layout: page
permalink: /who/
has_children: true
nav_order: 3
---
## Suggested content
- Key roles & responsibilities
- outlines leadership roles & who makes management
- community team "who's who" + other stakeholders
- Community members
- outlines team members, what they bring to the group, how they benefit from being part of the group, and special instructions for team members
- community leaders' directory, staff collaborators
## Bio-IT content
About the community
About the community management team
Stakeholders
- profiles of Toby & Renato
- list of other management
- Peer, Georg, Toby G
- description of Taskforce
- list of other key members
- EMBL Centres DONE
- Git Admins DONE
- survey info
- community overview
- GTLs with >50% computational activity
- expected increase
---
title: Why
layout: page
permalink: /why/
has_children: true
nav_order: 2
---
## Suggested content
- Community overview
- a description of
- what the community is
- who it's for
- what it aims to do
- Community value
- the shared goals of the community
- outcomes and impacts for individuals, research teams, centres, institutes, etc
- Personas
- resulting in a clearly articulated need/goal for each persona
## Bio-IT content
- mission statement DONE
- background DONE
- community overview from survey DONE
- timeline DONE
- personas DONE
- links to particular sections relevant to each persona