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From 2010.igem.org

	Home Team Colin Hoffman Jeremy Kemball Anna Kropornicka Bobak Hadidi Acknowledgements Team Profile Project BioMORTAR Website IMPtools Website IMPtools v1.0 Plasmid Designer Modeling Next Version Cooperation Press Newsletter Notebook Bootcamp Safety

Contents 1 Project Overview 1.1 Project Description 1.1.1 IMPtools 1.1.2 Plasmid Designer 1.1.3 Cell Modeling 1.2 Judging Criteria

Project Overview

The 2010 Illinois Software project, BioMORTAR, is a bacterial design suite composed of a vastly improved IMPtools, an automated plasmid designer, a modeling tool, and a user plasmid registry. More details to come later in the summer.

Project Description

The 2010 Illinois iGEM Tools Team is in the phase of constructing a program to design a plasmid in-silico for the user-specified host bacteria as well as model the growth of the designed cell.

The web-based program will begin by implementing the desired metabolic pathway computed by a greatly improved version of last year's project, IMPtools, then by determining the recommended enzymes for each reaction, and accessing the DNA sequence for it. In the meantime, the program will model the growth of the user specified bacteria with the new metabolic pathway to optimize the plasmid design. Finally, it will construct and display, with annotation, the advised plasmid(s) for the user as well as display important information on projected growth.

An additional function will be a program-based plasmid registry that not only allows for users to display, to others, what plasmids they hold in the lab, but it will also reference these stored plasmids to the other users looking to implement the generated plasmid design. In addition, it will have the option to adhere to the iGEM biobrick standards and will reference the biobrick database.

As a whole, the program will not only give the user the optimal plasmid design for the metabolic process, but it will project growth for the modified bacteria and connect the user with the other users storing the necessary plasmids.

IMPtools

Plasmid Designer

Cell Modeling

Judging Criteria

The requirements to earn a Bronze Mousepad are:

1. Register the team, have a great summer, and have fun attending the Jamboree.
2. Create and share a Description of the team's project via the iGEM wiki.
3. Present a Poster and Talk at the iGEM Jamboree.
4. Develop and make available via the Registry an open source software tool that supports synthetic biology based on BioBrick standard biological parts (remember, the iGEM judges will be looking for substantial team-based software projects).

The requirements to earn a Silver Mousepad, in addition to the Bronze Mousepad requirements, are:

1. Provide a detailed, draft specification for the next version of your software tool, or a second, distinct software tools project.

The requirements to earn a Gold Mousepad, in addition to the Silver Mousepad requirements, are:

1. Help another iGEM team by, for example, analyzing a Part, debugging a Device, or modeling or simulating a System.
2. Develop and document a new technical standard that supports the (i) design of BioBrick Parts or Devices, or (ii) construction of BioBrick Parts or Devices, or (iii) characterization of BioBrick Parts or Devices, or (iv) analysis, modeling, and simulation of BioBrick Parts or Devices, or (v) sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.
3. Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.