06 September 2010

textstream.blogspot.com has moved to blog.gerstein.info

This blog has moved to blog.gerstein.info .
The posts below are kept for simply archival purposes and to prevent broken links.

20 March 2010

My academic genealogy, back to Newton !

Link to the Mathematics Genealogy Project

Image of my academic genealogy back to Newton , with a mere 18 links ! (courtesy of C Chothia)

Text of the above (18 links to Newton)

**1.** Mark Gerstein
2. Cyrus Chothia UCL (+ R Lynden Bell)
3. Peter Pauling P 1931-2003
4. John Kendrew P 1917-1997
5. Max Perutz P 1914-2002
6. John Desmond Bernal RI 1901-1971
7. William Henry Bragg T 1862-1942
8. J. J. Thompson T 1856-1940
- - - I Lord Rayleigh T 1842-1919
9. Edward Routh P 1831-1907
10. William Hopkins T 1793-1866
- - -Augustus De Morgan (T) 1806-1871
11. Adam Sedgwich T 1785-1873
- - - William Whewell T 1794-1866
- - - John Hudson T 1773-1843
12. Thomas Jones T 1756-1807
- - - John Cranke T 1746-1816
13. Thomas Postlethwaite T 1731-1798
14. Stephen Whisson T ~ 1718-1783
15. Walter Taylor T 1700-1744
16. Robert Smith T 1689-1768
17. Roger Cotes T 1682-1716
**18.** Isaac Newton T 1643-1727
Isaac Barrow T 1630-1677
James Duport T 1606-1679

T: Trinity College; P: Peterhouse; RI Royal Institution, London; UCL: University College, London

13 February 2010

let. to ed. re. "Empty Archives" -- Nature

We read with great interest the recent article in Nature about the
difficulties in data sharing and archiving ("Empty Archives"). While the author discusses database archiving in detail, he neglects to consider the important archival role
served by academic journals. When it comes to archiving, journals are
more than disinterested third parties. They have historically been, and
continue to be, the central actors in scientific communication. As such,
journals should take the lead in devising and implementing standards
that will allow data from disparate fields to be shared and exchanged.
They should also embrace data sharing as part of the publication
process. Note that this is very much the viewpoint taken in the
companion article in the issue from the Toronto Data Release Workshop.

Although journals have historically sought to provide a permanent record
of scientific advance, many of the problems that we now face in relation
to data archiving and sharing stem from the fact that the publication
process with its varied, idiosyncratic formats often seems purposefully
divorced from this archiving role. It is time for journals to devise
universal structured versions of articles and appendices that
accommodate - and archive -- large data sets. This is no small task, and
it is no doubt larger than any one journal or editorial board. But
while daunting, such progress is necessary to preserve the value and
relevance of journals - and the fundamental service they provide - as we
move into a database-driven future.

Dov Greenbaum JD, PhD
Michael Seringhaus PhD
Mark Gerstein PhD

Above is an unpublished letter in response to:

Published online 9 September 2009 | Nature 461, 160-163 (2009) |
doi:10.1038/461160a Data sharing: Empty archives Bryn Nelson


Nature 461, 168-170 (10 September 2009) | doi:10.1038/461168a; Published
online 9 September 2009 Prepublication data sharing Toronto
International Data Release Workshop Authors

16 January 2010

Trips to Europe '09

Here I've collected various things related to some trips to Europe in 2009.

* Pictures

Flickr photos galleries from London in Jan., Belgium in Oct., and Paris & Cambridge in Dec. (The analogous links in picasa: London, Belgium, & Paris .)

In addition to the usual tourist shots, I took some fairly abstract photos and some more general "concept" ones. My photos also added significantly to my burgeoning McDonald's photo collection.

* Tags & Routes

I tagged my photos quite extensively. Here's a listing of some of my more commonly used tags on the trips. One 'tag group' that was particularly hard to shoot were the panoramas and nighttime photos , where I was aided by my trusty new Sony. Here's an almost 360' panorama of the Louvre.

As might be expected, I geotagged many of the photos as well; thus, each of these galleries is associated with a nice map link -- e.g. here's an one for Paris . The geotagging has the side benefit of providing some tracks of where I went, viz: walking around Paris, Paris to London (via Chunnel), & walking around London (not necessarily in order).

* Links & Lectures

Here's a general collection of links of random information associated with the trips.

Some lectures that I gave during the trips: 1a, 1b, 2, 3, 4

Some of my own cryptic internal IDs with yet more links: i0wtsysbio, i0gencwinter08, i0vib