a database of useful biological numbers

[Jorgensen, Paul Conrad]

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Dear all,  

I have a non-confocal post, but one that will hopefully be of interest
to this community.  A group of us in the systems biology department at
Harvard Medical have built a database to store useful biological numbers
( www.bionumbers.org ), such as cell and organelle sizes, diffusion
coefficients, protein concentrations, etc.  

We built the database because of a common realization of how many hours
it can take to find even the most trivial numbers in the literature.
And then once the number is found, where to store the information for
future use?  Bionumbers is more permanent and more searchable than
post-it notes.  We can't guarantee the accuracy of the numbers, only
that they are published values - the site is meant to rapidly connect
you to literature sources - a sort of Pubmed for numbers.

Please check out our database and mabye even enter some numbers you
would like to keep track of - all database users will benefit from your
entry.  The database is a long-term project of the department and will
be continually improved for the foreseeable future.  Any suggestions to
make the database more useful are very welcome ( [hidden email] ).


Paul

Paul Jorgensen, Ph.D.
Post-doctoral fellow, Kirschner Laboratory
Systems Biology, Harvard Medical School
200 Longwood Avenue, Alpert 536
Boston, MA, 02115 U.S.A.
Ph: (617)-432-2294
[hidden email]

[Salim, Asmat (salima)]

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear Paul

It seems exciting to have such a database. Although I have not yet explored it fully but it looks like we can have answers to many queries within minutes. If I face any difficulty in finding something, can I direct my queries to your email ?

Thank you

Asmat Salim, Ph.D.
Assist. Professor
Dr. Panjwani Center for Molecular Medicine and Drug Research
International Center for Chemical anc Biological Sciences
University of Karachi, Karachi, Pakistan
[hidden email]

 

 

 

 

 

 

<mailto:[hidden email]>  

 

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear all,

I have a non-confocal post, but one that will hopefully be of interest
to this community.  A group of us in the systems biology department at
Harvard Medical have built a database to store useful biological numbers
( www.bionumbers.org ), such as cell and organelle sizes, diffusion
coefficients, protein concentrations, etc.

We built the database because of a common realization of how many hours
it can take to find even the most trivial numbers in the literature.
And then once the number is found, where to store the information for
future use?  Bionumbers is more permanent and more searchable than
post-it notes.  We can't guarantee the accuracy of the numbers, only
that they are published values - the site is meant to rapidly connect
you to literature sources - a sort of Pubmed for numbers.

Please check out our database and mabye even enter some numbers you
would like to keep track of - all database users will benefit from your
entry.  The database is a long-term project of the department and will
be continually improved for the foreseeable future.  Any suggestions to
make the database more useful are very welcome ( [hidden email] ).


Paul

Paul Jorgensen, Ph.D.
Post-doctoral fellow, Kirschner Laboratory
Systems Biology, Harvard Medical School
200 Longwood Avenue, Alpert 536
Boston, MA, 02115 U.S.A.
Ph: (617)-432-2294
[hidden email]

[Andrew Resnick]

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

This is AWESOME!  Thanks!

Andy

At 01:21 PM 5/7/2008, you wrote:

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Dear all,
>
>I have a non-confocal post, but one that will hopefully be of interest
>to this community.  A group of us in the systems biology department at
>Harvard Medical have built a database to store useful biological numbers
>( www.bionumbers.org ), such as cell and organelle sizes, diffusion
>coefficients, protein concentrations, etc.
>
>We built the database because of a common realization of how many hours
>it can take to find even the most trivial numbers in the literature.
>And then once the number is found, where to store the information for
>future use?  Bionumbers is more permanent and more searchable than
>post-it notes.  We can't guarantee the accuracy of the numbers, only
>that they are published values - the site is meant to rapidly connect
>you to literature sources - a sort of Pubmed for numbers.
>
>Please check out our database and mabye even enter some numbers you
>would like to keep track of - all database users will benefit from your
>entry.  The database is a long-term project of the department and will
>be continually improved for the foreseeable future.  Any suggestions to
>make the database more useful are very welcome ( [hidden email] ).
>
>
>Paul
>
>Paul Jorgensen, Ph.D.
>Post-doctoral fellow, Kirschner Laboratory
>Systems Biology, Harvard Medical School
>200 Longwood Avenue, Alpert 536
>Boston, MA, 02115 U.S.A.
>Ph: (617)-432-2294
>[hidden email]

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

[Markus Rehm]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

This is a fantastic idea!

A comprehensive database like this will be a key requirement for the future
of experimental systems biology. We published a small scale database option
together with a systems model which allows direct comparability to timelapse
imaging data of apoptotic cell death kinetics
(http://systemsbiology.rcsi.ie/apopto-cell.html) . The potential to hook up
single cell data, "bionumbers", and systems models is immense.
Actually, most wet labs would have the possibility to obtain a lot more
"numbers". However, most experiments are still carried out qualitatively as
there very seldom was the requirement to determine e.g. intracellular
protein concentrations.

As it fits the topic, please forgive me to point out our publications
related to this:

Huber HJ, Rehm M, Plchut M, Düssmann H, Prehn JH.
APOPTO-CELL--a simulation tool and interactive database for analyzing
cellular susceptibility to apoptosis. Bioinformatics. 2007 Mar
1;23(5):648-50. Epub 2007 Jan 19.PMID: 17237051

H. Huber, G. Gomez Estrada, H. Dussmann, C. O'Connor, and M. Rehm Extending
the Explanatory Power of Live Cell Imaging by computationally modelling the
Execution of Apoptotic Cell Death
http://www.formatex.org/microscopy3/pdf/pp88-99.pdf

Rehm M, Huber HJ, Dussmann H, Prehn JH.
Systems analysis of effector caspase activation and its control by X-linked
inhibitor of apoptosis protein. EMBO J. 2006 Sep 20;25(18):4338-49. Epub
2006 Aug 24.PMID: 16932741

Looking forward to see Bionumbers growing!

Cheers
Markus

Dr. rer. nat. Markus Rehm
Biomedical Research Lecturer
Dept. of Physiology & Medical Physics
Royal College of Surgeons in Ireland
RCSI York House
York Street
Dublin 2
Ireland
 
phone: 00353 (0)1 4028563
email: [hidden email]


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Jorgensen, Paul Conrad
Sent: 07 May 2008 19:21
To: [hidden email]
Subject: a database of useful biological numbers

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear all,  

I have a non-confocal post, but one that will hopefully be of interest
to this community.  A group of us in the systems biology department at
Harvard Medical have built a database to store useful biological numbers
( www.bionumbers.org ), such as cell and organelle sizes, diffusion
coefficients, protein concentrations, etc.  

We built the database because of a common realization of how many hours
it can take to find even the most trivial numbers in the literature.
And then once the number is found, where to store the information for
future use?  Bionumbers is more permanent and more searchable than
post-it notes.  We can't guarantee the accuracy of the numbers, only
that they are published values - the site is meant to rapidly connect
you to literature sources - a sort of Pubmed for numbers.

Please check out our database and mabye even enter some numbers you
would like to keep track of - all database users will benefit from your
entry.  The database is a long-term project of the department and will
be continually improved for the foreseeable future.  Any suggestions to
make the database more useful are very welcome ( [hidden email] ).


Paul

Paul Jorgensen, Ph.D.
Post-doctoral fellow, Kirschner Laboratory
Systems Biology, Harvard Medical School
200 Longwood Avenue, Alpert 536
Boston, MA, 02115 U.S.A.
Ph: (617)-432-2294
[hidden email]

[Peter Gabriel Pitrone]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear all,

Everyone knows the answer is 42.

it's the question that matters.

Pete

On May 7, 2008, at 8:21 PM, Jorgensen, Paul Conrad wrote:

Search the CONFOCAL archive at

http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear all,  

I have a non-confocal post, but one that will hopefully be of interest

to this community.  A group of us in the systems biology department at

Harvard Medical have built a database to store useful biological numbers

( www.bionumbers.org ), such as cell and organelle sizes, diffusion

coefficients, protein concentrations, etc.  

We built the database because of a common realization of how many hours

it can take to find even the most trivial numbers in the literature.

And then once the number is found, where to store the information for

future use?  Bionumbers is more permanent and more searchable than

post-it notes.  We can't guarantee the accuracy of the numbers, only

that they are published values - the site is meant to rapidly connect

you to literature sources - a sort of Pubmed for numbers.

Please check out our database and mabye even enter some numbers you

would like to keep track of - all database users will benefit from your

entry.  The database is a long-term project of the department and will

be continually improved for the foreseeable future.  Any suggestions to

make the database more useful are very welcome ( [hidden email] ).

Paul

Paul Jorgensen, Ph.D.

Post-doctoral fellow, Kirschner Laboratory

Systems Biology, Harvard Medical School

200 Longwood Avenue, Alpert 536

Boston, MA, 02115 U.S.A.

Ph: (617)-432-2294

[hidden email]

Peter Gabriel Pitrone

Light Microscopy Facility

Max Planck Institute for 

Cell Biology and Genetics

Pfotenhauerstrasse 108

01307 Dresden, Germany

E-Mail: [hidden email]

[Rosemary.White]

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

This is mainly for the plant people, but has useful info for mouse people as
well.  Maybe you all mostly know about this, but it was new to me.

At bar.utoronto.ca you can see tissue-level expression of genes throughout
development, and cell-level expression in different organelles according to
accumulated data in various gene databases, mostly for Arabidopsis.  Some of
the localisations are based on experimental data, some on predictions.  I
imagine there will be a few corrections, but it's a great start, and a
really nice interface.

cheers,
Rosemary

Rosemary White                    [hidden email]
CSIRO Plant Industry            ph.     61 (0)2-6246 5475
GPO Box 1600                       fax.     [phone]
Canberra, ACT 2601
Australia

[Fernando Avila-Rencoret]

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Paul,

thank you very much for sharing the database.

Is it possible to get a direct link to pubmed (I know that you have the
Reference PubMed ID for some of them)

Can you make it a rule? (to submit a DIRECT clickeable  link to the source)

Are you planing to perform some data-mining on your database? (I love chilibot)
multifactorial analysis of the numbers? Clustering? etc.

thanks!

Fernando

Fernando Avila-Rencoret, MD
Department of Biomedical Engineering
Carnegie Mellon University