User:Ron Milo: Difference between revisions
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It is hard to define precisely. We think about them as the “model organisms” of numbers. A good BioNumber is one that will be useful for other people in the community. Examples of what we thought will be useful can be seen by browsing the database. If in doubt, you can always ask us or just add the number, we are sure it wouldn’t do any harm… | It is hard to define precisely. We think about them as the “model organisms” of numbers. A good BioNumber is one that will be useful for other people in the community. Examples of what we thought will be useful can be seen by browsing the database. If in doubt, you can always ask us or just add the number, we are sure it wouldn’t do any harm… | ||
High throughput data on mRNA levels, life times, protein-protein interactions or similar properties are better stored in a database of their own that we can happily point to from our section on “other databases of useful biological numbers”. | High throughput data on mRNA levels, life times, protein-protein interactions or similar properties are better stored in a database of their own that we can happily point to from our section on “other databases of useful biological numbers”. | ||
In properties where the value is known for many organisms (say number of chromosomes), we are interested in the values for the model organisms and the extreme cases that teach about the limits (say largest number of chromosomes in any animal). | |||
== Ideas in the pipeline == | == Ideas in the pipeline == | ||
Revision as of 12:33, 16 July 2007
BioNumbers - the database of useful biological numbers
Current version of BioNumbers database.
What is BioNumbers?
BioNumbers is a collaborative community effort to establish a database of useful biological numbers.
For example:
- How many ribosomes or mRNAs are in a cell (e.coli, yeast, mammalian or any other) ?
- The volume of different cells and organelles
- Concentrations and absolute numbers of ions and metabolites
- Generation times of different organisms
and many many other useful but too often hard to find numbers. Each property/number includes a reference, and other relevant information. We currently have a very rudimentary format based on the google documents collaboration tool (basically an excel-like sheet), but we hope to add graphical user interfaces with querying capabilities in the near future.
Please check out the current version of the BioNumbers database.
Some more explanation on what it is and where is it going to can be found below.
To join as a collaborator and contribute your favorite numbers to this effort please send an email to ron_milo@hms.harvard.edu or mike_springer@hms.harvard.edu or paul_jorgensen@hms.harvard.edu.
Motivation
Numbers are absolute and immutable entities. Biology is built on adaptation and flexibility. It is thus no surprise that concrete values for many biological properties are hard to find. Most quantitative properties in biology depend on the context or the method of measurement, the organism and the cell type. Yet it is clear that characteristic numbers and ranges are very useful tools to have available. The aim of this database is to be a repository for useful biological numbers, that gives a concrete value while supplying the relevant reference and comments that depict its domain of validity. We hope that you and others will find it useful and help to expand it and make it more accurate.
Interesting examples from BioNumbers
- Number of mRNAs in cell (total absolute number):
- Yeast - 15000 (BioNumbers index 339)
- Escherichia coli - 4000 (BioNumbers index 61)
- Number ATP to make 1 cell
- Escherichia coli - 55 billion (BioNumbers index 173)
- Minimal generation time:
- Vibrio natriegens - 9.8 minutes (BioNumbers index 231)
- Mutation rate per genome per replication:
- Escherichia coli - 0.0025 (BioNumbers index 310)
What qualifies as a good BioNumber?
It is hard to define precisely. We think about them as the “model organisms” of numbers. A good BioNumber is one that will be useful for other people in the community. Examples of what we thought will be useful can be seen by browsing the database. If in doubt, you can always ask us or just add the number, we are sure it wouldn’t do any harm… High throughput data on mRNA levels, life times, protein-protein interactions or similar properties are better stored in a database of their own that we can happily point to from our section on “other databases of useful biological numbers”. In properties where the value is known for many organisms (say number of chromosomes), we are interested in the values for the model organisms and the extreme cases that teach about the limits (say largest number of chromosomes in any animal).
Ideas in the pipeline
- The comparative tables builder: you will be able to choose your properties and and organisms of interest and get a table comparing the values. We hope this will make comparative studies much easier, and will lead to new insights into quantitative design principles. Blanks will denote where we need more data.
- The comperaVisulaizer: a graphical interface that will visualize values for different organisms and different properties that share the same units. Kind of like the scale of lengths showing the progression from molecules to galaxies
- Vote for the ten BioNumbers every high school biology graduate should know.
- Vote for the one hundred BioNumbers every college biology graduate should know.
Contribute a BioNumber
It is really easy. You can send us an email to be able to edit the source database. Alternatively you can just go here and we will put it in the database with an acknowledgment of your contribution.
How did it get started?
The BioNumbers database started as a joint effort by Ron Milo, Paul Jorgensen and Mike Springer at the systems biology department in Harvard. The effort was inspired by a comparison of values of key properties in bacteria, yeast and a mammalian cell in Uri Alon’s book – “Introduction to systems biology”. It is our hope that the database will facilitate quantitative analysis and reasoning in a field of research where numbers tend to be “soft” and difficult to vouch for.
Other databases dedicated to certain types of biological numbers
- CyberCell Project - statistics on the bacteria E.coli
- BRENDA - a database of enzyme properties
- Animal Genome Size Database - a database of animal genome sizes, chromosomes numbers etc.
Our "wish list" of BioNumbers (can you help find them?)
- Minimal known generation time of a photosynthetic organism
- Concentration of NADP and NADPH in chloroplasts and in cyanobacteria under normal illumination
- Concentration of ADP and ATP in chloroplasts and in cyanobacteria under normal illumination
- Number of ribosomes in a Hela Cell or other mammalian cell
- Number of ATP molecules consumed in making a yeast
- Number of ATP molecules consumed in making a Hela cell
A number you would like to see on BioNumbers?
Do you have a secret "wish list" of biological numbers you would like to know? Please tell them to us and we would try to find them and incorporate them as soon as possible. Go to add wishful number.
