Bob with Bioagents

Bob with Bioagents is a machine partner you can chat with about molecular biology and solve problems together. The system can be launched with two different interfaces, CLiC and SBGNViz below.

To launch the dialogue system, click on one of the buttons below, and wait 90 seconds to get a dedicated instance of the dialogue system. Once started, the dialogue session will appear on the page and you can start talking with the machine agent. When you are done, click the End Session button above the dialogue interface.

The dialogue system was last updated on July 10 2019.

Introduction Video

Below is an introduction video to the system with an example of formulating a hypothesis for "How does SB525334 decrease the amount of SMURF2?" (a hypothetical experimental observation) by talking with the machine partner, which turns your hypothesis into a mathematical model of biochemical mechansms over the course of the dialogue, and is able to verify that the model reproduces the observation of interest. Link: https://goo.gl/frRzst

The CLiC interface focuses on simple text-based dialogue with minimal graphical display.

The SBGNViz interface contains a large model canvas along with the dialogue panel, allowing richer graphical model building and analysis.

Talking with Bob

Assume you want to explain an experimental observation, or get some ideas for your next experiment. You can talk with the machine agent in some of the following ways:

  • Ask about drugs, transcription factors, miRNAs and their targets
  • Ask for mechanisms connecting molecular entities
  • Define an observation you would like to find an explanation for
  • Build up a model of a hypothesis by describing it in natural language
  • Ask about dynamical properties of the model being discussed

Both interfaces show example sentences you can say. While the system aims to support substantial linguistic variation, following the pattern of these sentences is in some cases more reliable.

The development of this system was funded under the DARPA Communicating with Computers program. The system was developed by a consortium of teams from Harvard Medical School, OHSU, Tufts, SIFT and IHMC.

Point of contact: Benjamin M. Gyori (benjamin_gyori [AT] hms.harvard.edu)