Knowledge Fair Table C - Build a Model Based on In-Vitro Data
Summary: In this workshop, you will build a predictive model based on in-vitro data using OpenTox web services using a Graphical User Interface (GUI) and via the command line. Several models can be built and inspected.
Objective:
Learn to handle searching facilities, data representation, and API of the OpenTox framework, specifically in the context of in-vitro data.
Steps:
1. Inspect data from US EPA's Toxcast Program.
2. Select in vitro assays based on correlation to an in-vivo endpoint.
3. Use the ToxCreate webapplication to create a model
a. Fill the data into an Excel Sheet
b. Create the model
c. Make a prediction
4. Create a model using the Opentox API
a. Locate data on the ambit webservice.
b. Create a model on the command line using curl.
c. Make a prediction.
Necessary Software and Data Files:
Please download and install the following software, if you bring your laptop:
- Microsoft Office (version 2003 or better) or a comparable Office Suite.
- Mozilla Firefox: http://www.mozilla.com/firefox, a web browser.
- curl: http://curl.haxx.se/download.html, a command line tool for accessing the OpenTox API. You have two options on Windows for this:
- Install curl natively. You may want to use this version.
- For more convenience, consider installing VMWare Player and run a small Linux environment under Windows! Just double-click the dsl-4.1.vmx file.
Please download the following data fiiles:
- ToxCast Data Utilities: http://www.maunz.de/opentox/ToxCastDataUtils.zip, summarized data in convenient Excel sheet form.
- Handout: http://www.maunz.de/opentox/Rhodes_WS_BUILD_IVM.doc, instructions for this Knowledge Fair table (will also be available at the table in printed form).
