# [Bio-IT Hackathon](https://git.embl.de/grp-bio-it/hackathons) Project Pitches

## 15:00 04-Jun-2019

### Participants / Group

1. Toby Hodges / Bio-IT - Zeller
2. Malvika Sharan / Bio-IT - Gibson
4. Jure Pečar <[e-mail]>
5. Spencer Du <[e-mail]>
6. Saudat Alishayeva <[e-mail]>
7. Dominik Kutra <[e-mail]>
8. Constantin Pape <[e-mail]>
1. Ivan Berest <[e-mail]>
1. Frauke Huth <[e-mail]>
1. Florian Huber <[e-mail]>
1. Aleksander Jankowski <[e-mail]>
1. Thea Van Rossum <[e-mail]>
1. Alejandro Riera Mainar <[e-mail]>
1. Holly Joynes <[e-mail]>
1. Tabea Rauscher <[e-mail]>
1. Ivica Lehotska <[e-mail]>

Attended the call:

* Eva Maria Geissen / Bio-modeling
* Renato Alves / Bork lab

### Pitches - Guidance

- **what is the problem you’re trying to solve/the end-product you’re trying to create?**
- **what do you hope to have achieved by the end of the hackathon?** Be realistic! The Hackathon will last just under seven hours - what tasks do you think could be completed in that time? (It’s ok if your project isn’t finished in the one day, but there should be some achievable targets for the hackathon itself.)
- **can this be divided into multiple tasks?** If you will have a team of multiple people, how could the project be divided among them? Will you pair people up to work on the objectives together? All work as one team? Work individually?
- **can you link to material that people should read** before and/or refer to during the hackathon?
- **what will people need to know before they start?** For example, would one need to be an expert R user to contribute? What packages/modules/tools should people be familiar with before the Hackathon begins?

### Do you like working with our GitLab system? Add your pitch as a new issue:

- [https://git.embl.de/grp-bio-it/hackathons](https://git.embl.de/grp-bio-it/hackathons)

### Don't want to write them down here or online? Send an email to Bio-IT:

- [[e-mail]](mailto:[e-mail])

## Pitches - Online

#### Pitch 1: Malvika Sharan

**Detail**

- Malvika has been interviewing members of the Bio-IT community over the past six months, talking about their career stories.
- She'd like to work with people to go through these interview transcripts and collect them together into stories
- narrative
- advice, top tips on working in/learning computational science
- what will be done at the hackathon?
- not so programming-related
- working to create content as a group
- assessing data from a survey
- 28 EMBL + 2 external interviews
- All the recordings are available on youtube (private) and exported the captions
- Everything will be accessible to those who would like to help create blog posts and articles with them
- Outcome:
- Different stories and posts with authorship
- Understanding of the community
- Work with Bio-It blog infrastructure

#### Pitch 2: Toby Hodges

**Detail**

**Image analysis with Python/Jython/Matlab/ImageJ**

- [Online unified materials](https://git.embl.de/grp-bio-it/image-analysis-training-resources)

- Aim to build training materials
- [Example page](https://grp-bio-it.embl-community.io/image-analysis-training-resources/modules/binarization.html)
- Different pages will focus on different topics
- Each page will have standard format
- Drop down menu at the bottom of the page to switch paltform for image analysis (e.g. python, jython, matlab etc.)
- There will be instructions, exercises etc. for diferent platform
- There is an infrastructure in place with template
- Problem: The current flowcharts are not displayed in some of the browsers
- Contributions can involve writing exercises, examples, adding new modules, expanding the existing modules etc.
- Outcome: play around with Jakyl, authorship on the materials, understanding of concept-base design of the training modules
- Materials will be available online

#### Pitch 3: Ivan Berest

**Detail**

- Scientific Pitch
- There are a lot of groups in EMBL/EBI/other sites, who are doing different things.
- The only way to see their work in papers
- Idea: Visual display of methods that different groups are working with
- centralized information of the method with all the internal resources, tools, experiments, groups etc.
- outcome: It will save new comers some time that are wasted in identifying relevant resources
- Why? - EMBL is open space and encourages exchange
- Technical part will involve: Backend (database, website, small search engine)

- Create an EMBL app
- At EMBL HD we have so many clubs, SA website is great but can hold only short relevant information.
- An app will provide easy access to different club with their rules, date, funding, etc.
- Secured app exist that are specific to a conference, you can register with a key
- The infomation can lay internally to secure the data
- What we need: People who have designed an app, or want to explore designing an app

#### Pitch 4: Toby Hodges

**Detail**

- Version control training material for Bio-IT
- We have beginner and intermediate level material which have been taught recently
- Feedback included that people would like some materials to refer back to
- We can fork GB materials, however it also stop at basics
- We want to expand by adding examples of merge reqest etc.
- Have more plan added about the git.embl.de
- Talk a bit about continuous integration
- We would in general interested in having people write any tutorial, but git will be a start

#### Pitch 5: Jure Pecar

**Detail**

- Problem we want to solve: Making people more aware of resource they ask for Vs. amount of resources they use
- Aim: graphical representation of cluster usage
- Bringing people who have R/Python skill for visualization of data from the database
- Goal
- Use this to develop materials for data visualization
- Create Shiny app
- Official R-based interface to slurm
- Training materials for slurm
- Group leaders can visualize the usage of resources from their members
- Curating data that is useful for others and present them to users in a useful manner
- Reference:
- Already available codes online/published
- People should know R libraries to interact to mysql and create a webpage with that

- Mike Smith created something for shiny based visualization, which can act as a basis for this project
- https://spinoza.embl.de/shiny/msmith/slurm-job-summary/
- source code here: https://git.embl.de/msmith/slurm_dashboard
- Outcome:
- We fixed all the bugs we found in the original R code https://git.embl.de/pecar/slurm_dashboard/tree/master
- We began work on some ideas that were discussed
- we want to continue working on these ideas

#### Pitch 5: Tabea Rauscher (through email)

**Detail**

- resources.embl.org

Community-driven open source visual library of icons for scientific figures, graphical abstracts and presentations

Scientific figures, graphical abstracts, presentations. They’re all based on icons scientists spend hours on drawing or dealing with copyrights issues. How about saving researchers these hours by bringing EMBL community together, and a creating a visual library of high quality icons available in .eps format? Icons that once created, can be reused, modified and recycled again and again by anyone? This resource would include icons starting from simple objects through DNA strands, organelles and model organisms, to lab equipment, and much more!

- What it would be about
- Creating icons together
- Create, share, improve: scientific objects to improve

- Why are we building it
- Mainly "Copyrights, Time, Quality, Capacity, Money"
- Scientists at EMBL suffer less when creating graphical outputs
- EMBL more recognizable because of the ‘embl look & feel’ of the visuals
- Better visibility of stratcomms/atc/designlab among embl scientific community
- Less support needed for scientists from us
- Getting to know scientists better
- Better quality of the figures (at embl)

- What are the best practices in creating scientific illustrations Library of objects in vector formats
- Templates for creating the objects in Adobe Illustrator, InkScape etc.
- Tutorial on how the library works and how to contribute
- Tutorial on using EMBL colour scheme
Best practice examples

- How you can get involved
- Join us on hackathon
- Curate images
- Add images
- Annotate images
- Use them!
- Share them!

- Contact:
- Tabea Rauscher (Design Team Lead): [e-mail]
- Aleksandra Krolik: [e-mail].

### What to expect on hackathon after this call?

- The recorded video will be shared with everyone
- People would be able to register for different ideas
- Notes from the call will be summarized into a blog
- Every relevant information will be posted here: [https://grp-bio-it.embl-community.io/hackathons/](https://grp-bio-it.embl-community.io/hackathons/)
- On the day we will start with a lightning talk
- The whole day will be uninterrupted time fo rthe team to work together
- Food and drinks will be available throughout the day
- We will end at 4:15 pm and have a short report back from each team
- At 5:00 pm we will head to the Bio-IT BBQ

### What would you like to see in hackathon? Add you ideas here:

- Jure volunteered to take care of the BBQ Fire!! (Yay!)

## More ways to pitch ideas (Tell your colleagues!):

### Did you miss the call? Add your pitches here:

- Pitch: Project name

- Pitch: Project name

- Pitch: Project name

- Pitch: Project name

(you can also send project ideas by email to [e-mail] or, if you're familiar with GitLab, submit a Merge Request to this repository: )