Key Review Articles
Title: Vector NTI Vs Genome Compiler
Description: This is an excellent review article explaining the benefits of Genome Compiler, as compared to Vector-NTI.
Title: Bricks and blueprints: methods and standards for DNA assembly
Description: This paper provides as excellent summary of DNA assembly methods, including Gibson Assembly, Golden Gate, ligase cycling reaction (LCR), modular cloning (MoClo), GoldenBraid, modular overlap-directed assembly with linkers (MODAL) and PaperClip.
Title: Development in the tools and methodologies of synthetic biology
Description: This review focuses on several significant tools, both classical and emerging, that the field of synthetic biology employs as part of a typical design cycle workflow. Building upon a design cycle template, the review is organized to explore prominent tools and research methodologies across three core areas: designing predictable biology (design), assembling DNA into bioparts, pathways and genomes (build), and rapid prototyping (test).
Title: European Commision’s Final Decision on Synthetic Biology
Description: A team of Scientific Committees published their opinion which aims to establish what Synthetic Biology is, what is its relationship to the genetic modification of organisms and what are the essential requirements of a science-based, operational definition of Synthetic Biology.
Title: New Directions: The Ethics of Synthetic Biology and Emerging Technologies
Description: The Presidential Commission for the Study of Bioethical Issues released a wide-ranging review of the emerging field of synthetic biology and issued 18 recommendations including a call for coordinated federal oversight of scientists working in both large institutions and smaller settings.
Title: Plant Synthetic Biology
Description: This review discusses the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes, including synthetic sensors, synthetic metabolic pathways, and synthetic genomes.
Title: Designing biological systems: Systems Engineering meets Synthetic Biology
Description: The review summarises the major achievements and categorises them according to a hierarchy of system levels. The hierarchy encompasses several levels of detail. Biological (macro-)molecules present the most detailed level (parts), followed by compartmentalised or non-compartmentalised modules (devices). In the next level, parts and devices are combined into functional cells and further into cellular communities.
Sigma® Life Science Resources
Title: Molecular Biology Handbook
Description: The handbook introduces classic molecular biology techniques (for bacteria, unless otherwise noted). Through each workflow, we provide background information, protocols, references to peer-reviewed literature, and help selecting reagents for your application.
Title: Cloning Manual (provided by Oxford Genetics)
Description: A review of molecular cloning: the set of techniques that are used by molecular biologists to insert a gene-of-interest into a vector capable of replication within the target cell.
Title: Cell Culture Manual
Description: A manual covering the basics of eukaryotic cell culture. Introduction to basic techniques, protocols, and product selection guides all in one place.
Title: qPCR Technical Guide
Description: A guide to understanding qPCR, designing probes and primers, optimizing and troubleshooting your assays.
Title: Metabolic Pathways Interactive Map
Description: This new edition of the iconic IUBMB-Sigma-Nicholson Metabolic Pathways Chart brings increased functionality to a canonical tool. Now, all metabolites, enzymes, and selected pathways are searchable and interactive.
Title: Custom Oligos Learning Center
Description: Oligonucleotide information, handling guidelines, protocols and tools designed to help you design the right custom products for your experiments.
Webinars and Videos
Title: CRISPR Webinars
Description: Video replays of our three most popular CRISPR webinars, covering introduction to gene editing, design, transfection, and validation.
Title: Genome Compiler Training Videos
Description: A collection of three videos showing how to perform the most common tasks in Genome Compiler – from the basics of getting started, to primer design and custom annotations.
Title: Doug Densmore’s Webinar on Bio-design Automation in Synthetic Biology
Description: This talk highlights Doug’s research efforts in the specification, design, assembly, verification, and data management involved in automating synthetic biology. These challenges are addressed by a suite of software tools which draw inspiration from Electronic Design Automation.
Posters & Publications
Title: Construction of a minimal nif gene cluster and computational modeling to optimize nitrogen fixation
Description: Poster presented as 2015 iGEM project to determine the minimal set of genes needed for nitrogen fixation and identify the ideal conditions for nitrogen fixation.
Title: NitroGENIUS: Engineering E. coli to Fix Nitrogen and Regulating Transcription with Light
Description: Poster presented as 2014 iGEM project to study nitrogen-fixing genes in a simpler environment (E.coli) and to work on a light repression system for gene expression. We want the nif cluster to be expressed when photosynthesis is not occurring, as oxygen poisons the nitrogenase enzyme.
Title: A CRISPR/Cas-GFP Vector for Rapid Expression Verification and Enrichment of Genome Edited Cells
Description: A poster describing our single plasmid design that ensures all GFP positive cells have the required CRISPR/Cas components.
Synthetic Biology Community
Description: SynBioBeta is the leading community of synthetic biology entrepreneurs, investors and thought leaders. Their annual events in San Francisco and London attract a large following and they also run smaller events on various topics in other cities around the world. The SynBioBeta digest is a newsletter published every two weeks full of synthetic biology news, views and commentary.
Title: The Bio-Design Automation Consortium
Description: The Bio-Design Automation Consortium, Inc. (BDAC) was organized to provide and promote education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation.
Title: Nona Research Foundation
Description: Nona Research Foundation, Inc. (NRF) was created to broaden participation, increase access, and advance innovation in the design, distribution, documentation, maintenance, and use of open-source software and tools in the fields of synthetic biology and bio-design automation.
Description: The International Genetically Engineered Machine (iGEM) Foundation is dedicated to education and competition, advancement of synthetic biology, and the development of open community and collaboration. The iGEM Foundation fosters scientific research and education through organizing and operating the iGEM Competition, and operating the Registry of Standard Biological Parts.
Description: Synberc is a major U.S. research program to make biology safer and easier to engineer. The research center includes some of synthetic biology’s leading academic and industrial scientists and researchers. Synberc strives to build the foundational tools and technologies needed to create innovative solutions to some of the most challenging problems of our time – including health care, energy and the environment.
Description: SynbiCITE is a pioneering Innovation and Knowledge Centre (IKC) dedicated to promoting the adoption and use of synthetic biology by industry.
Title: Synthetic Biology Congress
Description: A conference designed for experts working in genome engineering, technological developments, protein design, cell building, bio-manufacturing and gene editing.
Description: Biobuilder converts cutting-edge science and engineering into teachable modules for middle and high school students and teachers.
Title: The Registry of Standard Biological Parts
Description: The iGEM Registry is a growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems.
Title: International Association Synthetic Biology (IASB)
Description: Representing providers, users and consumers of synthetic biology, IASB aims at bringing this exciting scientific field to full potential by development of best practices and standards as well as through the promotion of biosecurity and biosafety.
Description: DIYbio’s mission is to establish a vibrant, productive and safe community of DIY biologists. Central to their mission is the belief that biotechnology and greater public understanding about it has the potential to benefit everyone
Synthetic Biology Tools
Title: Genome Compiler
Description: A free, web-based intuitive software platform for the rapid engineering of biology with its genomic manipulation tools and its optimal design experience, with an additional benefit of direct connections to an array of product and service providers.
Title: Design Automation Tools (by CIDAR at Boston University)
Description: A collection of open-source tools aimed at making synthetic biology more effective by integrating concepts from electronic design automation into the specification, design, and assembly of complex biological systems.
Title: Bioinformatics Toolbox
Link to Dr. Stothard’s Laboratory Website: http://www.ualberta.ca/~stothard/index.html
Title: Synthetic Biology Open Language (SBOL)
Description: The SBOL can be used to represent genetic designs through a standardized vocabulary of schematic glyphs as well as a standardized digital format.