This a brief guide designed to help those who are willing to contribute to ChassiDex by curating data.
All organisms on ChassiDex are color coded.
- Red: Gram-negative bacteria
- Blue: Gram-positive bacteria
- Purple: Fungi
- Green: Others, including plants and mammalian systems
Organisms on ChassiDex are stored species-wise. The genus name and specific epithet are required to store the organism. Different strains/variants of the organisms need not be represented here.
The safety level (BSL 1-4) helps researchers decide if their lab is equipped enough to safely handle the organism. This also determines various use-cases for the organism.
Tags are usually one-phrase descriptions that help group organisms and provide a very brief description. While filling in data, select all relevant tags from the already used ones and add new tags if possible.
Briefly mention all uses and potential synthetic biology applications of the organism.
Mention different strains of the organisms and their specific uses.
Organisms have different life-cycles and reproductive stages. Briefly mention the different life cycle stages for the organism. They may be as simple as growth and binary fission, or be complex, involving sporulation etc.
Doubling time of an organism is an important factor to be considered while working with an organism. Mention the doubling time of the organism, and the conditions under which it can be achieved.
Factors such as temperature, pH and availability of certain nutrients play a role in growth of the organism. Briefly mention the optimal conditions for these factors.
In order to get started with an organism, a researcher would obviously need a starter culture. This may be obtained from stock collection centers or other labs that are willing to share cultures of the organism. Make a list of such sources from which one may obtain a culture.
List plasmid vectors that can be used to work with this organism and where one may obtain them from.
Different DNA parts such as promoters, reporters, coding sequences, ribosome binding sites, and replication origins help synthetic biologists to compose circuits and some of these parts are host specific. Mention DNA parts that can be used to work with this organism. You can find DNA parts at the iGEM Registry: http://parts.igem.org/Main_Page
Mention and link to different protocols that are to be followed for maintaining a culture of this organism. This includes optimal conditions for subculturing and long term storage.
Mention protocols for introducing your genetic constructs into the cells of the organism.
Mention other protocols that may be required to put the organism to use.
This section contains various bioinformatics and computational biology data that can be used to understand the organism better. They include:
Link or provide accession number to genome sequence of the organism.
Tables indicating codon bias in organisms help optimize genes for expression in the particular organism.
Genome scale metabolic models can help run useful metabolic simulations and carry out modelling to guide experimental work.
Online resources exist for specific organisms, such as SubtiWiki for Bacillus subtilis and Pombase for Schizosaccharomyces pombe. If such online resources/forums exist for the organism, mention them and provide a link.