JBEI-ICE, part registry platform and tools

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsisseeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code (http://code.google.com/p/gd-ice/) , a hosting site for community-driven open source projects.

 

Apps Collections for Synthetic Biology

 

Synthetic biology which is inspired by “plug-and-play” concept is supported by standardized biobricks and also computational tools for analysis and optimization [1]. Here are bio-apps collections for you. Personally Tinkercell and UNAFold are mostly used.

Circuit design and simulation
 Biojade http://web.mit.edu/jagoler/www/biojade/
 Tinkercell http://www.tinkercell.com/Home
 Asmparts http://soft.synth-bio.org/asmparts.html
 ProMoT http://www.mpimagdeburg.mpg.de/projects/promot
 GenoCAD http://www.genocad.org/genocad/
 GEC http://research.microsoft.com/gec
 TABASCO http://openwetware.org/wiki/TABASCO#TabascoSimulator
 Hy3S http://hysss.sourceforge.net/index.shtml
Circuit optimization
 Genetdes http://soft.synth-bio.org/genetdes.html
 RoVerGeNe http://iasi.bu.edu/∼batt/rovergene/rovergene.htm
DNA and RNA design
 Gene Designer https://www.dna20.com/index.php?pageID=220
 GeneDesign http://www.genedesign.org
 UNAFold http://www.bioinfo.rpi.edu/applications/hybrid/download.php
 mfold http://mfold.bioinfo.rpi.edu/download/
 DINAMelt http://dinamelt.bioinfo.rpi.edu/
 Vienna RNA package http://www.tbi.univie.ac.at/∼ivo/RNA/
 Vienna RNA web servers http://rna.tbi.univie.ac.at/
 Zinc Finger Tools http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
Protein design
 Rosetta http://www.rosettacommons.org/main.html
 RAPTOR http://www.bioinformaticssolutions.com/products/raptor/index.php
 HHpred http://toolkit.lmb.uni-muenchen.de/hhpred
 Modeler http://salilab.org/modeller/
 PFP http://dragon.bio.purdue.edu/pfp/
 Autodock 4.2 http://autodock.scripps.edu/
 HEX 5.1 http://webloria.loria.fr/∼ritchied/hex/
Integrated workflows
 SynBioSS http://synbioss.sourceforge.net/
 Clotho http://biocad-server.eecs.berkeley.edu/wiki/index.php/Tools
 Biskit http://biskit.sf.net

 

Suggested pages listing useful bio-apps maybe you will like in synthetic biology research:

  1. WikiGenes Toolbox ( http://www.wikigenes.org/e/art/e/187.html). As a free on-line tutorial edited by people all around the world, WikiGenes has spirits of Linux: open-source, sharing, interest, so is WikiGenes-Synthetic-Biology page. It enables you fast-learn what is synthetic life.
  2. OpenWetWare (http://openwetware.org/wiki/Computational_Tools).
  3. JCVI (http://www.jcvi.org/cms/research/software/#c614). This page is from J. Craig Venter Institute.

 

— end &&reference

[1] Marchisio, M. A., & Stelling, J. (2009). Computational design tools for synthetic biology. Current Opinion in Biotechnology, 20(4), 479-485. Retrieved from http://www.sciencedirect.com/science/article/pii/S0958166909001001

Computer Program Enrich Understandings to RNA motifs

DNA carries and passes the genetic information with nucleotides sequences, but in some virus RNA does the job instead of DNA.  In addition, the 3D structure of RNA, RNA motif, shows more various roles in cellular functions. It means that only with sequence information we cannot fully understand the RNA roles and functions. Detecting and … Read moreComputer Program Enrich Understandings to RNA motifs

FX: an RNA-Seq analysis tool on the cloud

FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ∼160,000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of … Read moreFX: an RNA-Seq analysis tool on the cloud