Shenzhen_BGIC_0101_2013 Download - Shenzhen_BGIC_0101

Shenzhen_BGIC_0101_2013

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Genovo

Welcome to Genovo World. We are Shenzhen_BGIC_0101_2013 team. Please step to project page for better view. :)

What we do is

NeoChr

Neochr module would assist users to grab related genes in different pathways manually, to rewire genes’ relationship logically*, and to replace genes with ortholog that score higher*.

NucleoMod

NucleoMod is a module to modity CDS sequence of genes which generated by Neochr module. This module contains 5 plugins: CRISPR design, erase enzyme site, create enzyme site, codon optimization, repeat smash. All of these plugin is allow user to change or optimize the gene. After NucleoMod operation, the next step is SegmMan to design synthestic method according to the length of chromosome.

SegmMan

The synthesizer or synthesis chip can up to 3kb DNA sequence with high accuracy, but chromosome is not that short. SegmMan can settle this problem, it splits chromosome into 30k fragments, after parsing its exited enzyme sites, continues segmentation into 10k and 2k fragments. In 10k and 2k level, its will add vector homologous region and design enzyme sites.

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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 http://gmod.org/wiki/JBrowse.

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.sh # 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

perl5
php5 ( for REST api and backend server )
Apache
Linux ( Tested on Debian )
git ( for version control plugin )
Biopython and UNAFoldt ( for chip plugin )
Blast+ ( for NucleoMod Plugin )
Chrome, Firefox, and IE10 is recommand

Permissoin Requirment

You Need change apache permission by Edit /etc/apache2/envvars

  export APACHE_RUN_USER=`whoami`
  export APACHE_RUN_GROUP=`whoami`

And

  sudo chown `whoami`:`whoami` /var/lock/apache2/
  sudo /etc/init.d/apache2 restart

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

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

Install Genovo

Copy plugins/, server/ to Jbrowse.

Install NucleoMod Plugin

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

Or you can Install From: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

Install Chip Plugin

Download and install UNAFoldt and Biopython from:

UnaFold http://dinamelt.rit.albany.edu/download.php

Biopython: http://biopython.org/DIST/docs/install/Installation.html

install version control plugin

git is needed

Any other Plugins is portable

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Genovo Server Side Tutrorial

Folder Structure :

./data/    
   |-NeoChr_5_add          # NeoChr Plugin, name as "NeoChr_{weekday}"
   |---01.whole2mega       # SegmMan plugin  data
   |---02.globalREmarkup   # SegmMan plugin  data
   |---03.mega2chunk2mini  # SegmMan plugin  data
   |---chip_data           # chip design
   |---names               # prefix for search
   |---seq                 # crc32 encode refsequence  name path
   |-----d7f
   |-------417
   |---------f1
   |---tracks             # track display in browser
   |-----gene             # track cluster
   |-------NeoChr         # Genome Name 
   |-----part
   |-------NeoChr
   |-----Transcript
   |-------NeoChr

 ./server/
   |-bin
   |---chip_new           # create new chip data 
   |-----ols-pool-generation-script
   |-------output-oligos-and-primers
   |---GetPrice           # fetch enzyme price
   |---segmentation       # SegmMod plugin 
   |-config               # plugins config data
   |---features            
   |---geneset
   |---globalREmarkup
   |---markers
   |---Optimize
   |-doc                    # document about plugins
   |-lib                    # library used
   |-pathway                # pathway data used 
   |-REST                   # end-side REST implement
   |-------chip
   |-------features
   |-------modify
   |-------Segmentation
   |-------stats
   |---config
   |-rewire

REST API

base_url = server/REST/index.php

# output genes data by refname and pos
GET base_url/features/SearchByLocation?refname&start&end   
POST base_url/features/delete

# output git verison control for unroll data
GET base_url/stats/version/(?<dataset>w+)

# get pathway resource
GET base_url/pathway/nav

# create and decouple from order genelist data
POST base_url/decouple?refname&

# add loxp, centremele, ARS and so on
POST	/modify/Add

#  SegmMod plugin 
POST 	/Segmentation/globalREmarkup
	        /Segmentation/mega2chunk2mini
	        /Segmentation/whole2mega
GET  	/Segmentation/info
	
# Nucleo plugin
POST     /NucleoMod

# chip plugin
POST	/chip/chip

GET 	/stats/config 

# for get downloadable data information
GET /data/info

Besides, our server side implement is flexable. User can config server side data for power usage.

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Medals Requirement

##Bronze Medal

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
Overview of project
3 Present a Poster and Talk at the iGEM Jamboree.
4 Develop and make available via the The Registry of Software Tools an open source software tool that supports synthetic biology based on BioBrick standard biological parts
- Our software in Github

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

1.A Provide a detailed, draft specification for the next version of your software tool.

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

1.B Provide a second, distinct (yet complementary) software tools project.

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.

2 Provide a demonstration of their software either as a textual or video tutorial made available on their wiki.

Textual tutorial

Gold Medal

1 Have another team utilize the software developed by your team. You must clearly show how your software was used and the results that were obtained.

We have software team Shenzhen_BGIC_ATCG to use the second module to design their genes.
SC2.0 project also try out SegmMan module on chrVII’s segmentation.
2 .A Outline and detail how your software effects Human Practices in Synthetic Biology.