User:Ron Milo

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 user interface (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.

Where did it come from

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.

The bioNmbers DB is currently hosted on google docs, we expect it to move to a more friendly format soon.

Dedicated databases with focused useful biological numbers

BRENDA - a database of enzyme properties Animal Genome Size Database - a database of animal genome sizes, chromosomes numbers etc.enzyme properties

our "wish list" of bionumbers (can you help find them?)

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Some interesting numbers from our database

Ron Milo Website

bioNumbers highlights