Skip to content

Commit

Permalink
Update workshop_2024/hackathon.md and workshop_2024/schedule.md
Browse files Browse the repository at this point in the history
  • Loading branch information
@haeussma
haeussma committed Sep 15, 2024
1 parent 3a4b426 commit 55c486e
Show file tree
Hide file tree
Showing 4 changed files with 67 additions and 22 deletions.
14 changes: 14 additions & 0 deletions docs/workshop_2024/general.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
# 5th EnzymeML Workshop

**24.-26.9.2024, Hotel Jagdschloss Niederwald, Rüdesheim, Germany**

**Organizers:** Carsten Kettner, Jürgen Pleiss, Santiago Schnell
**Supported by:** Beilstein Institute, Frankfurt, and the EU COST Action COZYME

---

We are glad to invite you to our **5th EnzymeML Workshop** at the Hotel Jagdschloss Niederwald in Rüdesheim (Germany) on **24.-26.9.2024**. Rüdesheim can conveniently be reached by train from Frankfurt airport (1½ h). During the three-day meeting, we will demonstrate and explore the application of our EnzymeML platform during the first EnzymeML Training Course, discuss challenges (especially data acquisition and data analysis), and jointly plan the next steps. We would be glad if you and your co-worker(s) would participate, contribute a dataset for testing, give a talk, and contribute to the discussion.

The **[Beilstein-Institut](https://www.beilstein-institut.de/)** will cover conference costs, and the **[EU COST Action COZYME](https://cozyme.eu/)** "Pan-European Network on Computational Redesign of Enzymes" (CA2116), will cover accommodation and travel costs.

Please find more details at on the [Beilstein workshop website](https://www.beilstein-institut.de/en/projects/strenda/meetings/5th-enzymeml-workshop/)
26 changes: 24 additions & 2 deletions docs/workshop_2024/hackathon.md
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,25 @@
# Hackathon
### Hackathon: Managing Your Own Data with EnzymeML Tools

## Description
This session is designed to familiarize participants with the EnzymeML tools through an interactive workshop. It begins with an introduction to the EnzymeML Suite, a comprehensive grapgical application for creating and visualizing EnzymeML documents. The session will also highlight interoperability with various libraries, showcasing integrations with tools like MTPHandler, NMRPy, and Catalax to enhance versatility and functionality. Thereafter, brought datasets will be read in, with the EnzymeML tools [`chromatopy`](https://fairchemistry.github.io/chromatopy/) for chromatographic measurements, [`mtphandler`](https://fairchemistry.github.io/MTPHandler/), as well as [`nmrpy`](https://nmrpy.readthedocs.io/en/latest/?badge=latest)

__Requirements__:

To participate in the hands-on session, the following hardware and software are required:

- **Laptop** with an up-to-date operating system (e.g., recent Windows, macOS, or Linux operating system)
- [**Anaconda** installation](https://docs.anaconda.com/anaconda/install/):

Anaconda simplifies installing and managing Python, Jupyter, and essential tools. It bundles everything you need, including numerous libraries, making it perfect for beginners and advanced users.

__Bringing Your Own Data__:

We provide a selection of prepared datasets for use during the workshop. If you plan to utilize your own data, see the following list of supported devices and file formats:

- Plate reader data
- BioTek, Magellan, Multiskan Spektrum, Multiskan Skyhigh, or Spectramax 190, Tecan Spark
- Chromatographic data
- refere to the supported formats and data preparation in the [documentation of `chromatopy`](https://fairchemistry.github.io/chromatopy/supported_formats/)
- NMR data
- FIDs of NMR measurements (e.g., Bruker, Varian)

You should also bring data from calibration measurements if applicable.
48 changes: 28 additions & 20 deletions docs/workshop_2024/schedule.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,59 +2,67 @@

## 24.9.2024

### Session 1: Status and application of the EnzymeML platform
### Session 1: Status and Application of the EnzymeML Platform

| Time | Talk |
|-------|--------------------------------------------------------------------------------------------------|
| 9:00 | **Jürgen Pleiss**:<br>Welcome and overview on EnzymeML activities |
| 9:30 | **Jan Range, Max Häussler, Torsten Giess**:<br>Demonstration of EnzymeML tools |
| 9:30 | **Jan Range, Max Häussler, Torsten Giess (U.Stuttgart)**:<br>Demonstration of EnzymeML tools |
| 12:00 | _End of session 1 and lunch_ |

### Session 2: Hackathon: managing your own data with EnzymeML tools
### Session 2: Hands-on: Managing Your Own Data

| Time | Talk |
|-------|--------------------------------------------------------------------------------------------------|
| 13:30 | **Jan Range, Max Häussler, Torsten Giess & all participants**:<br>Read in, and analyze your own datasets |
| 13:30 | **Jan Range, Max Häussler, Torsten Giess & all participants**:<br>Read in, analyze, and publish your own datasets |
| 17:00 | _End of session 2_ |
| 17:15 | _Excursion_ |
| 19:30 | _Dinner_ |

## 25.9.2024

### Session 3: Acquisition of data and metadata
### Session 3: Acquisition of Data and Metadata

| Time | Talk |
|-------|--------------------------------------------------------------------------------------------------|
| 9:00 | **Johann Rohwer**:<br>LabNexus: an open-source enzyme kinetics data automation web application |
| 9:45 | **Marilize Le Roes-Hill**:<br>Expanding the enzyme 'reactome' via high-throughput experimentation – is reproducibility an issue? |
| 9:00 | **Johann Rohwer (U.Stellenbosch)**:<br>LabNexus: An open-source enzyme kinetics data automation web application |
| 9:45 | **Marilize Le Roes-Hill (CPUT, Cape Town)**:<br>Expanding the enzyme ‘reactome’ via high-throughput experimentation – is reproducibility an issue? |
| 10:30 | _Coffee break_ |
| 11:00 | **Nicole Jung**:<br>tba |
| 11:45 | **Katrin Rosenthal**:<br>Challenges and solutions for digital (un)structured data in biocatalysis |
| 11:00 | **Nicole Jung (KIT, Karlsruhe)**:<br>tba |
| 11:45 | **Katrin Rosenthal (Constructor U., Bremen)**:<br>Challenges and solutions for digital (un)structured data in biocatalysis |
| 12:30 | _End of session 3 and lunch_ |

### Session 4: Data analysis, modelling, optimization, and design of experiment
### Session 4: Data Analysis, Modelling, Optimization, and Design of Experiment

| Time | Talk |
|-------|--------------------------------------------------------------------------------------------------|
| 14:00 | **Zvjezdana Findrik**:<br>Modelling approach in the biocatalytic process optimization and design |
| 14:45 | **Andreas Bommarius**:<br>Biocatalysis in multiphase reactors |
| 14:00 | **Zvjezdana Findrik (U.Zagreb)**:<br>Modelling approach in the biocatalytic process optimization and design |
| 14:45 | **Andreas Bommarius (Georgia Tech, Atlanta)**:<br>Biocatalysis in multiphase reactors |
| 15:30 | _Coffee break_ |
| 16:00 | **Jenny Andexer**:<br>tba |
| 16:45 | **Sebastian Höpfl**:<br>Optimal experimental design in biocatalysis - from Gaussian processes towards Bayesian statistics |
| 16:00 | **Jenny Andexer (U.Freiburg)**:<br>When cascades turn into cycles - from cofactor supply to regeneration |
| 16:45 | **Sebastian Höpfl (U.Stuttgart)**:<br>Optimal experimental design in biocatalysis - from Gaussian processes towards Bayesian statistics |
| 17:30 | _End of session 4_ |
| 19:30 | _Dinner_ |

## 26.9.2024

### Session 5: Infrastructure: what comes next
### Session 5: Infrastructure: What Comes Next?

| Time | Talk |
|-------|--------------------------------------------------------------------------------------------------|
| 9:00 | **Carine Vergne-Vaxelaire**:<br>High throughput screening data on enzyme activity: a first proposal for user-friendly data integration into EnzymeML workflow |
| 9:45 | **Frank Bergmann**:<br>tba |
| 9:00 | **Carine Vergne-Vaxelaire (Genoscope, Évry)**:<br>High throughput screening data on enzyme activity: a first proposal for user-friendly data integration into EnzymeML workflow |
| 9:45 | **Frank Bergmann (U.Heidelberg)**:<br>Future-proofing software infrastructure: enhancing EnzymeML with WebAssembly |
| 10:30 | _Coffee break_ |
| 11:00 | **Ulrike Wittig**:<br>Using EnzymeML to exchange and publish reaction kinetics data in SABIO-RK |
| 11:45 | **Carsten Kettner**:<br>Extending STRENDA DB light |
| 11:00 | **Ulrike Wittig (HITS, Heidelberg)**:<br>Using EnzymeML to exchange and publish reaction kinetics data in SABIO-RK |
| 11:45 | **Carsten Kettner (Beilstein I., Frankfurt)**:<br>Extending STRENDA DB light |
| 12:30 | _End of session 5 and lunch_ |

### Session 6: Outlook and planning
### Session 6: Outlook and Planning

| Time | Talk |
|-------|--------------------------------------------------------------------------------------------------|
| 16:00 | **Santiago Schnell (U.Notre Dame)**:<br>Round robin study on measuring enzyme reactions |
| 16:30 | **Mehdi Davari (IBP, Halle)**:<br>Critical Assessment of Enzyme Design |
| 17:00 | _Final remarks_ |
| 17:30 | _End of session 6_ |
| 19:30 | _Dinner_ |
1 change: 1 addition & 0 deletions mkdocs.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ site_name: EnzymeML Training Course
nav:
- Home: index.md
- EnzymeML Workshop 2024:
- General: workshop_2024/general.md
- Programme: workshop_2024/schedule.md
- Hackathon: workshop_2024/hackathon.md
- DIY:
Expand Down

0 comments on commit 55c486e

Please sign in to comment.