Events

Online Jaqpot Hackathon - Take your research from the bench to the community by making your models available as a web service

Webinar, Hackathon, Training, Workshop (organized by NanoCommons)
3 Jun 2020 / Online

Activity details

On Wednesday, June 3rd 2020, the NanoCommons team, in a joint initiative with the NanoSafety Cluster, is offering an interactive online workshop on nanotoxicity prediction.  

Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, you will learn how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file.

Jaqpot is a computational platform for in silico modelling of chemical compounds, that provides both access to its services both over a User Interface (GUI) and an Application Programming Interface (API). It is a cloud-ready application that uses the benefits of Java, R and Python, having incorporated functionality by various established and open-source machine learning and data analysis toolkits, while algorithms in any programming algorithm can be added to Jaqpot.

Target audience: Bench scientists looking into creating models based on their data and making them available to the community.

Expectation: Willing to learn new things and active participation in the interactive training session.

The webinar will take place from 10:00 till 13:15 h CEST.

Preliminary Agenda:

10:00 - Introduction round and background to the NanoCommons platform

10:10 - Preparation for the hands on session - setting up anaconda

10:30 - Introduction to Electronic Laboratory Notebooks (ELN)

10:45 - Introduction to the NanoCommons KnowledgeBase (NC KB)

11:00 - Introduction to the Jaqpot suite of tools

11:20 - Virtual coffee break (incl time for Q&A) 

11:30 - Jaqpot hands-on session

11:40 - Jupyter: Setting up + brief introduction to what you need to get started in python 

11:50 - Importing and exploring the dataset

12:00 - Basic preprocessing

12:10 - Creating a local model and its evaluation

12:20 - Short break

12:25 - Uploading your model to Jaqpot: You now have your web service! - Exploring your model on Jaqpot (adding information, QMRF report, Discussions)

12:35 - Using the model to get predictions on the web and in Python

12:45 - Explore the platform, create more models and give us your ideas

13:10 - Summary and Wrap up

13:15 - Virtual drinks and time for personal Q&A


Feel free to join and please do not forget to register here asap so we can tailor the workshop for your needs: Registration - Hackathon 3rd June 2020 

Please, be aware that some personal information may be collected for statistical purposes, however, in blinded and anonymous way.

Shortly before the webinar, registered participants will receive an email with some preparation instructions. 

Please, use this link for joining the sessionhttps://global.gotomeeting.com/join/504904269 

Feel free to redistribute this information within your projects and networks. We are happy to have as many participants as possible and to help the community with the FAIRification of their data by using Jaqpot model applications to previously annotated CSV files.

The NanoCommons team will be happy to answer your questions and to guide you in your requests!

Organisations involved

The University of Birmingham (UoB)
Edelweiss Connect GmbH (EwC)
United Kingdom Research and Innovation (UKRI)
National Technical University of Athens (NTUA)
BioNanoNet (BIONANONET)
Universitat Salzburg / Paris Lodron University of Salzburg (PLUS)
BIOMAX Informatics AG (BIOMAX)

Resources & Training materials

Presentation
Jaqpot Hackathon - Training materials
Martin Himly, PLUS Iseult Lynch, UoB Dieter Maier, Biomax Philip Doganis, NTUA
3 Jun 2020
Abstract:

Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, you will learn how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file.

Jaqpot is a computational platform for in silico modelling of chemical compounds, that provides both access to its services both over a User Interface (GUI) and an Application Programming Interface (API). It is a cloud-ready application that uses the benefits of Java, R and Python, having incorporated functionality by various established and open-source machine learning and data analysis toolkits, while algorithms in any programming algorithm can be added to Jaqpot.

The following training materials were used:

1. Intro to NanoCommons by Martin Himly, PLUS

2. Electronic Lab Notebooks by Iseult Lynch, UoB

3. NanoCommons Knowledgebase by Dieter Maier, Biomax

4. Jaqpot Suite by Philip Doganis, NTUA


Target audience: Data providers, Bioinformaticians, Data modellers, Data owners, Students, Researchers
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: UoB, UKRI, NTUA, BIONANONET, PLUS, BIOMAX
Presentation

Links and additional materials

Documents:
Instructions_for_Installing_Anaconda.pdf - info for Anaconda installation
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