• About
• People
  • Fuels Synthesis Leadership
  • Fuels Synthesis Staff
• Groups
  • Biofuels Pathways
  • Metabolic Engineering
  • Biofuels Toxicity & Tolerance
  • Host Engineering
  • Synthetic Biology
• Publications
• Resources
  • Resources
  • Tools

 

Tools

BioInformatics:

GLAMM allows a user to visualize functional data on metabolic networks and facilitates the determination of pathways and genes for retrosynthesis of biofuel molecules. Representing functional data on metabolic networks can aid a researcher in rapid hypothesis generation when determining the cell-wide impact on genetic perturbations or the metabolic response to altered conditions, such as increased concentrations of toxic biofuel product.

The MicrobesOnline genome database contains over 700 prokaryotic genomes. All genomes are analyzed through the VIMSS genome pipeline. We use publicly available sequence analysis tools and databases to search for homologs (NCBI BLAST, SwissProt, COG) and protein domains (InterPro), to assign gene ontologies (Gene Ontology Consortium) and EC numbers and to map the metabolic pathways (KEGG). We then link the orthology relationships between genes, predict operon structures and regulon networks.

BioCAD:

With the emergence of parts registries (along with their associated characterization data) and automated DNA assembly methods, BioCAD tools are beginning to play an increasingly important role. DeviceEditor currently serves as a graphical user interface for designing (combinatorial) DNA assemblies and for generating the corresponding input files required for j5 (see below). Biological parts are mapped to iconic representations either via copy/paste from a highlighted sequence region in Vector Editor or from portions of local Genbank-format sequence files. The spatial arrangement of these icons determines the design of the (combinatorial) DNA construct(s) to be assembled. DeviceEditor provides access to controlling the assembly strategy, Eugene design specification rules the j5-specific parameters used when designing the assembly strategy.

j5 automates the design of standardized scar-less DNA parts assembly, for the construction of plasmid vectors. We have developed the software package j5 that automates the design of these DNA assembly protocols, determining the most cost-effective assembly strategy (e.g. direct synthesis vs. PCR) as it does so. Furthermore, j5 can condense multiple assembly protocols together, allowing multiple independent DNA construction projects to be executed in parallel in the same 96-well format plates. j5 also produces high-throughput liquid handling robotics platform command scripts to further automate the execution of the DNA assembly protocols.

Clotho is for engineering synthetic biological systems and managing the data which is used to create them. It also provides a mechanism to begin the process of creating standardized data, algorithms, and methodologies for synthetic biology.

Chemical synthesis of custom DNA made on order calls for software streamlining the design of synthetic DNA sequences. GenoCAD can be used to design protein expression vectors, artificial gene networks, and other genetic constructs composed of multiple functional blocks called genetic parts. By capturing design strategies in grammatical models of DNA sequences, GenoCAD guides the user through the design process. By successively clicking on icons representing structural features or actual genetic parts, complex constructs composed of dozens of functional blocks can be designed in a matter of minutes. GenoCAD automatically derives the construct sequence from its comprehensive libraries of genetic parts.

TinkerCell is a project aimed at collaborative modeling of biological systems. TinkerCell is a drawing program for biological network design; modeling and simulation platform; C++ library for creating new drawing programs; modular model construction program; and, collaborative model construction/analysis framework.

This site introduces the Systems Biology Workbench (SBW), an open source framework connecting heterogeneous software applications. SBW is made up of two kinds of components: (1) modules - these are the applications that a user would use; there is a wide collection of model editing, model simulation, and model analysis tools; and (2) framework - the software framework that allows developers to cross programming language boundaries and connect application modules to form new applications.