Open PHACTS for Academia: Using the Open PHACTS Discovery Platform in undergraduate and postgraduate teaching (London, UK)
The sixth Open PHACTS Community Workshop was held at Burlington House, Piccadilly, London on 26th June 2014.
The Workshop focussed on introducing members of the academic community to the Open PHACTS Discovery Platform, and showing them how to use it within their research and teaching workflows. The morning session featured an introduction to the Open PHACTS Discovery Platform and Application Ecosystem, and presentations on applications and academic use cases that use the Open PHACTS API. The afternoon session involved engaging attendees with interactive discussions (see below) and workshops on technical aspects of using workflow tools and code to query the Open PHACTS API.
Download the Community Workshop agenda.
Session I: Open PHACTS for research and teaching
The Open PHACTS Discovery Platform (Bryn Williams-Jones, Connected Discovery)
The Open PHACTS Application Ecosystem (Lee Harland, Connected Discovery)
Apps: ChemBioNavigator (Katrin Stierand, University of Hamburg)
The ChemBioNavigator (CBN) is one of the example applications in the Open PHACTS project. It allows the user to visualize the chemical and biological space of a molecule group in a chemically-aware manner. The physico-chemical properties of molecular groups can be plotted against each other. Given compounds or compound sets are annotated with properties from the integrated pharmacological data. Starting from a compound, new sets of molecules can be generated by similarity search or substructure search. Additionally, it is possible to search for a set of compounds which are active against one target. In a hands-on session, the participants have the possibility to try the functionality and different workflows of the CBN.
Apps: PharmaTrek (Jordi Mestres, IMIM)
Jordi Mestres, IMIM
Academic use case: ErbB signaling (Daniela Digles, University of Vienna)
This presentation will show the application of the Open PHACTS Discovery Platform for a research question in academia. The topic of this use-case is the Epidermal growth factor receptor (ErbB) signaling pathway, which is associated with cancer and neurodegenerative diseases. Using the Open PHACTS API with the workflow tool KNIME, pharmacology data for proteins in the ErbB signaling pathway was collected and visualized in a heat-map. ChEBI terms for the compounds were used to restrict the visualisation to compounds of interest. The resulting workflow can be re-used for any other available pathway, as a tool to get a quick overview on available data.
Academic use case: Programming in the Life Sciences (Egon Willighagen, Maastricht University)
Course Material for Programming in the Life Sciences at Maastricht on GitHub.
- A six day course
- Accounts and API keys
- Communication from within HTML
- Converting the results into HTML
- Coding standards
- APIs and Web Services
- First screenshots
- Another screenshot
- Two more projects
- Sixth project screenshot
- Open PHACTS LDA usage
Interactive sessions for developing Open PHACTS apps, and querying Open PHACTS with KNIME, Pipeline Pilot, Python and MOE.
Session II: Using the Open PHACTS API
How to use the Open PHACTS API (Christine Chichester, SIB)
Connecting to the Open PHACTS API via Python / Pipeline Pilot (Robert Campbell, GSK)
- Visit the Open PHACTS Pipeline Pilot Community Portal
- Open PHACTS Component Collection 2.0
- Download Python here.
- Online Python Interpreter and documentation and tutorials
- URI: http://beta.openphacts.org/1.3/structure/substructure?app_id=your_app_id&app_key=your_app_key&searchOptions.Molecule=CC
- Online json viewer
Developing your own app (Ian Dunlop, University of Manchester)
Information about compounds, targets, pathways and more is available through the Open PHACTS API. This allows scientists to retrieve data and use it in their own applications.
This session will show you how to use the API and how to integrate it with your own applications. We will use the OPS.js library to create a standalone web page to show information about compounds in a web browser. Data from the Open PHACTS API can also be displayed in pre-formatted HTML using widgets from the biojs project and we will look at what is available and how to use them.
You will need:
- A modern browser (Firefox, Chrome, Opera, IE9+)
- A text editor
- OPS.js, Jquery & compound.html (zipped) (all here as ZIP file).
- API keys (don’t worry, we will provide some for you if necessary)
Using the Open PHACTS API with KNIME (Daniela Digles, University of Vienna)
KNIME is an open source analytics platform, which can be used to build workflows without the need of programming knowledge. The Open PHACTS OPS-Knime nodes developed by Ronald Siebes (VU Amsterdam) aim to incorporate the Open PHACTS API to KNIME.
This session will show you how to build you own workflows using the API through the OPS-Knime nodes. You will need:
- KNIME Analytics Platform
- OPS-Knime (available from GitHub or as zip file here). To install the OPS-Knime nodes, unzip them in the plugins folder of your KNIME installation.
Open PHACTS and MOE, Google Spreadsheet (Lars Richter, University of Vienna)
Implementation of OpenPHACTS API within MOE (Molecular Operating Environment)
- Chemical Computing Group Homepage
- Download the SVL file (zipped)
- Run the SVL file within MOE (MOE2012)
Implementation of Open PHACTS API within Google Spreadsheet (You need to be logged in with your Google Account)
- Google Spreadsheet
- Make a copy of the Spreadsheet “File|Make a copy”
- Start the tool within the copy with “OpenPHACTS|PharmacologyByTarget”