JBEI Research Tools
Please remove DNA Constructor from the list.
Please remove DNA DIVA from the list.
Here are brief descriptions for the following tools:
j5
http://j5.jbei.org
Recent advances in Synthetic Biology have yielded standardized and
automatable DNA assembly protocols that enable a broad range of
biotechnological research and development. Unfortunately, the
experimental design required for modern scar-less multipart DNA
assembly methods is frequently laborious, time-consuming, and
error-prone. A cloud-based software tool, j5, automates the design of
scar-less multipart DNA assembly protocols including SLIC, Gibson,
CPEC, and Golden Gate. The key innovations of the j5 design process
include cost optimization, leveraging DNA synthesis when
cost-effective to do so, the enforcement of design specification
rules, hierarchical assembly strategies to mitigate likely assembly
errors, and the instruction of manual or automated construction of
scar-less combinatorial DNA libraries. j5 can be used to build
combinatorial libraries and applied to the preparation of linear gene
deletion cassettes. These innovations save researchers time and
effort, reduce the frequency of user design errors and off-target
assembly products, decrease research costs, and enable scar-less
multipart and combinatorial DNA construction at scales unfeasible
without computer-aided design. The j5 software has been exclusively
licensed to TeselaGen Biotechnologies for commercial use and
distribution.
DeviceEditor
http://j5.jbei.org
A cloud-based bioCAD software tool, DeviceEditor provides a graphical
design environment that mimics the intuitive visual whiteboard design
process practiced in biological laboratories. The key innovations of
DeviceEditor include visual combinatorial library design, direct
integration with scar-less multi-part DNA assembly design automation,
and a graphical user interface for the creation and modification of
design specification rules. DeviceEditor liberates researchers from
DNA base-pair manipulation, and enables users to create successful
prototypes using standardized, functional, and visual abstractions.
Open and documented software interfaces support further integration of
DeviceEditor with other bioCAD tools and software platforms.
DeviceEditor saves researcher time and institutional resources through
correct-by-construction design, the automation of tedious tasks,
design reuse, and the minimization of DNA assembly costs. The
DeviceEditor software has been exclusively licensed to TeselaGen
Biotechnologies for commercial use and distribution.
VectorEditor
https://public-registry.jbei.org/static/vesa/VectorEditor.html
An open source, cloud based, DNA sequence editing, annotation, and
analysis tool.
The public instance of the JBEI Registry
https://public-registry.jbei.org/
An open source, cloud based, DNA part, plasmid, microbial strain, and
Arabidopsis Seed online repository with physical sample tracking
capabilities. Integrated online tools include DNA sequence editing and
annotation (VectorEditor) and auto-aligning sequencing trace files
against a template.
PR-PR Laboratory Automation Platform
http://prpr.jbei.org/
Open source and cloud-based, PR-PR allows researchers to use
liquid-handling robots effectively, enabling experiments that would
not have been considered previously. After minimal training, a
biologist can independently write complicated protocols for a robot
within an hour.
JOSH H.
1001 Proteomes
http://1001proteomes.masc-proteomics.org/
The 1001 Proteomes portal provides a simple way to browse changes to proteins
caused by non-synonymous single nucleotide polymorphisms (nsSNPs) in
accessions or natural strains of Arabidopsis thaliana.
MASCP Gator
http://gator.masc-proteomics.org/
The MASC Proteomics Subcommittee have developed a proteomics aggregation
utility called the MASCP Gator, that queries and aggregates information from a
variety of online Arabidopsis proteomic resources.
Plant Protein Alignment and Phosphorylation Resource
http://ppapr.org/
PPAPR shows both observed and predicted phosphorylation sites with an
alignment of related sequences so you can see what sites are conserved and
whether phosphorylation at a homologous site is observed or predicted.
PENDING details:
JBEI Download server - Steve Singer and/or Patrik D'Haeseleer
MPROPHET - not sure what this is, POC is (probably) Chris Petzold
TDesign - don't know what this is, POC might be Tim Thimmaiah (don't know
> who
> this is), or his supervisor (don't know who that is)
Technoeconomic Wiki - Daniel