Bio-IT issueshttps://git.embl.de/groups/grp-bio-it/-/issues2021-12-08T16:22:02Zhttps://git.embl.de/grp-bio-it/blog/-/issues/1Alternative theme for the blog2021-12-08T16:22:02ZRenato AlvesAlternative theme for the blogThe current blog template doesn't make an efficient use of screen space, particularly at high resolutions.
Tables also render quite poorly and there's a big emphasis on the top image which is rarely relevant.
Themes below obtained fro...The current blog template doesn't make an efficient use of screen space, particularly at high resolutions.
Tables also render quite poorly and there's a big emphasis on the top image which is rarely relevant.
Themes below obtained from: https://themes.gohugo.io/
Some possible alternatives listed below (please edit and add more):
- [ ] https://themes.gohugo.io/themes/hugo-theme-cleanwhite/
- [ ] https://themes.gohugo.io/themes/syna/https://git.embl.de/grp-bio-it/grassroots/-/issues/8Success stories2021-11-22T10:46:03ZLisanna PaladinSuccess storiesFrom the OLS call with Emmy, Dave and Jason - specific about grassroots:
- [ ] collect success stories to showcase the grassroots project
- [ ] question the "always available" message
Other ideas:
- [ ] start a discussion with the comm...From the OLS call with Emmy, Dave and Jason - specific about grassroots:
- [ ] collect success stories to showcase the grassroots project
- [ ] question the "always available" message
Other ideas:
- [ ] start a discussion with the community about how to evaluate projects in light of open and FAIR science
Editing milestone Week 15 to include this.OLS-4 Week 15https://git.embl.de/grp-bio-it/grassroots/-/issues/7Feedback from collaborators2021-10-25T09:07:00ZLisanna PaladinFeedback from collaboratorsThis issue will serve to collect the feedback of collaborators about:
- This project structure and plan,
- The grassroots initiative as a whole,
- Suggestions on how to further develop Bio-IT as a community rather than a service.This issue will serve to collect the feedback of collaborators about:
- This project structure and plan,
- The grassroots initiative as a whole,
- Suggestions on how to further develop Bio-IT as a community rather than a service.https://git.embl.de/grp-bio-it/grassroots/-/issues/5Contributors acknowledgement2021-10-13T08:45:53ZLisanna PaladinContributors acknowledgementThe [grassroots webpage](https://bio-it.embl.de/grassroots-consulting/) states that grassroot consultants are distinguished by the grass 🌱 icon in [EMBL chat](https://chat.embl.org/) and [EMBL GitLab](https://git.embl.de/). We should:
- ...The [grassroots webpage](https://bio-it.embl.de/grassroots-consulting/) states that grassroot consultants are distinguished by the grass 🌱 icon in [EMBL chat](https://chat.embl.org/) and [EMBL GitLab](https://git.embl.de/). We should:
- Check if that's true, and how this is done
- Trigger automatic updates every time we update the contributors table
- Can we link the grassroots page through the icons?
- Can we represent the skills through additional icons / add badges?OLS-4 Week 15https://git.embl.de/grp-bio-it/grassroots/-/issues/4Table of grassroots experts2021-10-13T08:32:18ZLisanna PaladinTable of grassroots expertsThe current table of grassroots contributors is available in the [Bio-IT website](https://bio-it.embl.de/grassroots-consulting/).
The data there is outdated, meaning that some people may have left EMBL or even changed field.
We should:
...The current table of grassroots contributors is available in the [Bio-IT website](https://bio-it.embl.de/grassroots-consulting/).
The data there is outdated, meaning that some people may have left EMBL or even changed field.
We should:
- Contact the people listed there and ask them if they are still willing to participate
- Collect contacts from other people interested
- Ask them to list/revise their skills description according to the keywords
- Add a column for free text to allow them to provide additional details about their expertise
- Ask them to list/revise their preferred communication channelOLS-4 Week 10https://git.embl.de/grp-bio-it/grassroots/-/issues/3List of skills keywords2021-10-25T06:42:40ZLisanna PaladinList of skills keywordsThe skills list should describe the computational (and computational-related) expertise at EMBL.
This will serve as a standardised way of tagging experts in the grassroots project, but also to tag available training materials.
It shoul...The skills list should describe the computational (and computational-related) expertise at EMBL.
This will serve as a standardised way of tagging experts in the grassroots project, but also to tag available training materials.
It should be inspired by the list of skills we included in the [Data Sciences survey](https://git.embl.de/grp-datasci-training/biocomp-survey/-/blob/main/src/biocomp_survey), reported here for reference:
- Using specialised research software,
- Programming languages,
- Command-line computing,
- Exploratory data analysis and visualisation,
- Statistics and machine learning,
- Benchmarking bioinformatics tools,
- Cluster computing,
- Computational workflow management,
- Cloud computing,
- Image analysis,
- Biological modelling,
- Biological networks analysis,
- Data management and curation,
- Text mining,
- Software project management,
- Web technologies,
- GPU computing,
- System administration
At a later stage, the relationship between skills could be represented through a tree. Alternatively, staff roles can be represented through collection of skills.OLS-4 Week 10https://git.embl.de/grp-bio-it/grassroots/-/issues/2Roadmap2021-12-03T16:00:39ZLisanna PaladinRoadmap# Project mission and summary
The **Bio-IT Grassroots** initiative aims at bringing together members of EMBL's bio-computational community through reciprocal assistance on a wide range of topics. It serves as a platform to **support int...# Project mission and summary
The **Bio-IT Grassroots** initiative aims at bringing together members of EMBL's bio-computational community through reciprocal assistance on a wide range of topics. It serves as a platform to **support internal collaboration and consultation at EMBL**.
The activity was initiated in 2019 and it currently includes a table of EMBL **personnel available for consultation, respective topics of expertise and preferred communication channels**. The [grassroots webpage](https://bio-it.embl.de/grassroots-consulting/) also includes instructions on how to get involved, and states that grassroot consultants are indicated by the grass 🌱 icon in [EMBL chat](https://chat.embl.org/) and [EMBL GitLab](https://git.embl.de/).
The purpose of this project is to reactivate and improve the Bio-IT Grassroots initiative, by updating the relative data, advertising it, recruiting new members and acknowledge their contribution. The possibility of organising recurring or special events with these aims will be explored. Significant milestones will be established as control-points of the project progression. This project progression is monitored and supported through participation to the [forth cohort of the Open Life Sciences initiative](https://openlifesci.org/ols-4).
This issue is our roadmap. It's a place to start navigating the plan, or update and manage it. Check out the different milestones listed below.
# Roadmap
## 1. [OLS-4 Week 5](https://git.embl.de/grp-bio-it/grassroots/-/milestones/1)
Project initiation and documents setup.
- [x] Init the project repository
- [x] Establish main milestones in the project roadmap
- [x] Write README as landing page for the project
- [x] Add project license
- [x] Add project Code of Conduct
- [x] Add contribution guidelines and invite contributors
## 2. [OLS-4 Week 10](https://git.embl.de/grp-bio-it/grassroots/-/milestones/3)
Check project progress in the middle of the OLS program.
- [x] Create consistent list of keywords to represent grassroots experts' skills, see #3
- [ ] Update table of contributors, see #4
- [ ] Check 🌱 acknowledgment system, see #5
- [ ] Create expertise-specific chat channels
## 3. [Bio-IT Hackathon](https://git.embl.de/grp-bio-it/grassroots/-/milestones/2)
Opportunity to collaborate with the community and present the project progression. [Notes](https://pad.bio-it.embl.de/PNQSqqNPSqeir0uqWdoewg).
- [x] Recruit Hackathon organising committee (possibly to represent all groups, at leats make sure that it has been advertised in all expertise-specific channels)
- [ ] Tag all courses listed in the [workshops GitLab group](https://git.embl.de/grp-bio-it-workshops) with the skills keywords
- [x] Propose Hackathon activity (not mandatory, still an idea for TODO even after the event): each group should revise the training materials available and identify gaps
## 4. [OLS-4 Week 15](https://git.embl.de/grp-bio-it/grassroots/-/milestones/4)
Check project progress and OLS results at the end of the OLS program.
- [ ] Expand acknowledgment system (skills specific icons? badges?), see #5
- [ ] Establish a routine to update the table, recruit members and advertise grassroots
- [ ] Draw a plan for a grassroots-themed event
- [ ] Collect success stories, see #8https://git.embl.de/grp-bio-it/grassroots/-/issues/1OLS-4 documents2021-10-19T15:35:40ZLisanna PaladinOLS-4 documentsThis issue lists the documents and useful links from the [Open Life Sciences - OLS program](https://openlifesci.org/ols-4). Bold links are document produced in the project and strictly related to Grassroots, while others are useful links...This issue lists the documents and useful links from the [Open Life Sciences - OLS program](https://openlifesci.org/ols-4). Bold links are document produced in the project and strictly related to Grassroots, while others are useful links.
- [**GitHub OLS-4 Grassroots issue**](https://github.com/open-life-science/ols-4/issues/4)
- [**Self-assessment notes**](https://docs.google.com/document/d/1YtQ-EoltN-_4D85vfnnscfS4DQJEp2iWrKyCtXWEz1Y)
- [**Vision statement notes**](https://docs.google.com/document/d/19ukhbcNGoRctSG77dfdX_7XkEosf1hnVGy0cH4K354g)
- [**Compare and contrast assignment**](https://docs.google.com/document/d/17rClfffzxalOa4Rk-MJqs_5Yxb5-MD8aDYDInaoilqc) about current and desired community interactions and value exchanges
- [**Open Canvas**](https://docs.google.com/presentation/d/1qENlnOuE8hJltrQBVz6T_x1iH5wiyFRSNuFlMTe5z94/edit#slide=id.p)Lisanna PaladinLisanna Paladinhttps://git.embl.de/grp-bio-it/docs/-/issues/10Navigation breaks after two levels of depth2020-07-15T14:26:21ZToby HodgesNavigation breaks after two levels of depthleft-hand menu and link path at top of page doesn't work well for pages lower than depth two. Fix or, if we have to, reorganise to avoid.left-hand menu and link path at top of page doesn't work well for pages lower than depth two. Fix or, if we have to, reorganise to avoid.Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/docs/-/issues/8transparent background for favicon2019-09-02T14:35:17ZToby Hodgestransparent background for faviconToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/docs/-/issues/7Review request: site layout2019-08-15T16:01:45ZToby HodgesReview request: site layout@ext.hertweck I'd like to hear your thoughts on the JustTheDocs layout that I've adopted for these community docs.
Please take a look at both the built pages themselves and the source Markdown files. The latter contain additional tags i...@ext.hertweck I'd like to hear your thoughts on the JustTheDocs layout that I've adopted for these community docs.
Please take a look at both the built pages themselves and the source Markdown files. The latter contain additional tags in the YAML header that we will (hopefully) use in the future to make it possible for readers to quickly find things that are most relevant/interesting to them and their community.Kate HertweckKate Hertweckhttps://git.embl.de/grp-bio-it/docs/-/issues/6Review request: community member personas2019-08-15T15:58:10ZToby HodgesReview request: community member personas@ext.hertweck I'd love to hear your thoughts on https://grp-bio-it.embl-community.io/docs/why/personas/ Though I acknowledge that you're limited by lack of familiarity with our local community, perhaps the archtypes described are univers...@ext.hertweck I'd love to hear your thoughts on https://grp-bio-it.embl-community.io/docs/why/personas/ Though I acknowledge that you're limited by lack of familiarity with our local community, perhaps the archtypes described are universal enough for you to provide insight. I'm certainly interested in your perspective.
- do the characters describe resonate with you?
- based on your experience, are these accurate representations?
- what/who am I missing?
- do you think it's feasible to combine the novice/competent practitioner PhD & PostDoc into one persona? These are the two with the most overlap at the moment and I'm not sure if there's an important difference in their needs/motivations that I need to capture via two separate personas (personae?)Kate HertweckKate Hertweckhttps://git.embl.de/grp-bio-it/docs/-/issues/5need a way to browse tagged pages2019-08-13T13:45:38ZToby Hodgesneed a way to browse tagged pageshttps://git.embl.de/grp-bio-it/docs/-/issues/3add `target_audience` field to page front matter2019-08-13T13:43:35ZToby Hodgesadd `target_audience` field to page front matterwaiting for #2waiting for #2https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/59Workshop for image data quality control2019-07-24T09:51:00ZChristian TischerWorkshop for image data quality controlIt would be good to combine modules into a workshop that focusses on image data handling and quality control.
The point is to be able to judge whether an image acquired on a microscope is of sufficient quality.It would be good to combine modules into a workshop that focusses on image data handling and quality control.
The point is to be able to judge whether an image acquired on a microscope is of sufficient quality.Christian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/51Figures2019-07-18T07:31:56ZChristian TischerFigures@pape @halavaty @stamper @hossain
I made a Google Slides document for figures:
https://docs.google.com/presentation/d/1ZEzX8YrsCq6sAW6T5hEUkM7RYOyVNfpiafSo-b9VC3U/edit?usp=sharing@pape @halavaty @stamper @hossain
I made a Google Slides document for figures:
https://docs.google.com/presentation/d/1ZEzX8YrsCq6sAW6T5hEUkM7RYOyVNfpiafSo-b9VC3U/edit?usp=sharinghttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/49Unification of used images in trainig material2019-07-04T13:11:11ZDominik KutraUnification of used images in trainig material@stamper @pape and me have been working a bit on the Python training material during the first Annual Bio-IT Hackathon.
One of the outcomes is a re-organization of the already existing [Python training material](https://git.embl.de/grp-...@stamper @pape and me have been working a bit on the Python training material during the first Annual Bio-IT Hackathon.
One of the outcomes is a re-organization of the already existing [Python training material](https://git.embl.de/grp-bio-it/image-analysis-with-python/). Previously, it was one long Jupyter Notebook. We want to break it up into more digestible bits. The idea is then to link to static/interactive notebooks from the relevant "activity" section if python is chosen.
It is already very nice that all teaching material (I mean the language agnostic parts that only work with concepts) in this repo follows the same structure.
I know that one of the ideas of this repo is to provide a set of example images that are free to use for everyone. This is great of course. I just want to make a point for not using different images in the example teaching materials.
The benefit I see for users is that they don't get distracted by peculiarities of new images in every concept they have to grasp.
It could still be part of exercises to apply concepts to different images to better understand the effects.
What are your opinions on using the same image (or set of images) in all teaching examples?
Related:
* [issue tracking restructuring of Python teaching material](https://git.embl.de/grp-bio-it/image-analysis-with-python/issues/6)https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/46Jupyter notebooks for Python2019-07-04T08:05:01ZDominik KutraJupyter notebooks for PythonIn the context of python courses it would be great to refer to Jupyter examples
**Plan**:
* Create new repo with Jypyter notebooks, modeled after the concept maps
* Link to repo with example Jupyter Notebooks
* Binder for interactive s...In the context of python courses it would be great to refer to Jupyter examples
**Plan**:
* Create new repo with Jypyter notebooks, modeled after the concept maps
* Link to repo with example Jupyter Notebooks
* Binder for interactive session
* Also have code examples after selecting Python in drop-downhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/36Further material2019-06-12T10:42:11ZChristian TischerFurther material- Tischi's iBiology Talk
- MOOPS- Tischi's iBiology Talk
- MOOPSChristian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/34Literature2019-06-11T19:03:12ZChristian TischerLiterature- https://cecas.clemson.edu/~stb/ece847/internal/cvbook/ch02_pixproc.pdf- https://cecas.clemson.edu/~stb/ece847/internal/cvbook/ch02_pixproc.pdfChristian TischerChristian Tischer