Shenzhen bgic 0101 2013

Genovo is a Computer-Aided Design(CAD) tool to create genome denovo and would assit users to reconstruct chromosome biodevice, modify its sequence and design segmentation for assembly on their bent.

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Welcome to Genovo World. We are Shenzhen_BGIC_0101_2013 team.

What we do

install Guid

Our software are totally based on JBrowse which is next-generation of GBrowse. If you have install JBrowse, just pull git and use.

Install JBrowse

To install JBrowse, see the main JBrowse wiki at

For Short Description:

  • unzip the Download file in www root folder (/home/www is recommand and do not use /var/www/ as that need root permission)
  • cd jbrowse
  • ./ # Install all perl package needed with cpan, If all goes well, you can open http://localhost/jbrowse/index.html?data=sample_data/json/volvox

Software Requirment

Permissoin Requirment

Writable data, plugin/tmp_data, server/tmp_data, jbrowse_conf.json

Executable ./bin/ ./server/bin/ ./plugin/bin

Install NucleoMod Plugin

NucleoMod depend on Blast+, So if you use Debian based System: apt-get install ncbi-blast+

Or you can Install From:

Install Chip Plugin

Download and install UNAFoldt and Biopython from:

install version control plugin

git is needed

Any other Plugins is portable

File System

   |-bin              # JBrowse's exec
   |-data             # Genovo default output 
   |-extlib           # All perl 5 Library
   |-plugins          # JBrowse defaulte plugins folder
   |---Genovo         # Genovo plugin for JBrowse
   |-server           # Server side for JBrowse
   |---bin            # Server side exec
   |-----gaspserver   # chip plugin
   |-----GetPrice     # get enzyme's price
   |-----segmentation # SegmMan Plugin
   |---config         #  Genovo Server side config 
   |---doc            # Genovo Document
   |---lib            # Genovo library Needed
   |---pathway        # Pathway Data need by NeoChr Plugin
   |---REST           # Servers side REST implement
   |---rewire         # Logic genes data for next version 
   |---system         # REST implement

Medals Requirement

Bronze Medal

Note: Our giant software aims at operating Biobrick of device level based on synthesized DNA fragments. But for biobrick level, the second module can also assist users to design genes, such as deletion of EcorI, XbaI, SpeI, PstI, Not I in the CDS, codon optimization and repeat smash.

Silver Medal

As our project is so large and extensible greatly, at least 5 ideas can't be realized due to time limitation.

For the third module SegmMan, we have a complementary design & synthesis method OLS chip synthesis(link), so that Genovo is compatible for both synthesizer and chip.

Textual tutorial

Gold Medal


  • Web-based server for public to use
  • Software assessment and comparison with Biostudio.
  • Regional workshop



We use SBOL as one of the output of first module to describe the genes in new created pathway.

Design of BioBrick Parts or Devices :

Construction of BioBrick Parts or Devices :