Google Scholar

On the Lane library web-page:

Link from Google Scholar to FindIt@Stanford

You now can set preferences in Google Scholar to show "Find It @ Stanford Med" links, which connect you to Lane's online journals. This is the equivalent of the Stanford button in PubMed:

1) Connect to Google Scholar.

2) Click on Scholar Preferences to the right of the search box.

3) Check the box "Stanford University Medical Center (Find It @ Stanford Med)"

4) Click the Save Preferences button and continue searching.

5) Look for links in your search results labeled Find It @ Stanford Med Note that when on campus, you will also see links to "Find It @ Stanford" -- this version is provided by the main campus library system.

Inteins

What are inteins? Doug mentioned them to me today, and I had never heard of them. The short answer is that they are like introns, but in proteins. They splice themselves out of their host protein, and they only exist in single celled organisms, AFAIK. I think this pretty much means we have seen everything possible happen in biology now, bar reverse translation, which I am still not convinced does not exist. I can't find any really good reviews, but this paper is OK.
http://www.pubmedcentral.gov/articlerender.fcgi?tool=pmcentrez&artid=23508

Useful Python functions

Recently, I have been using these functions a lot. Maybe they will be of use to others.
These functions:

• sort a list of objects by an attribute, eg sort_by_attr(people, 'name')
  
• sort a list of objects by a list of attributes eg sort_by_attrs(people, ['lastname','firstname']
  
• print out all of the attributes of an object.
  

Read more

In the bleak bleak perl days, I might have made a list of blast hits as a dictionary of dictionaries, eg hit[gene1][gene2] = 10. Of course it's much neater to do it like this
hit = Container()
hit.gene1 = gene1
hit.gene2 = gene2
hit.score = score
Then you can sort by score, gene1, gene2 etc etc..

def sort_by_attr(seq,attr):
  """stably sort by an attribute"""
  seq2 = [[getattr(s,attr),i,s] for i,s in enumerate(seq)]
  seq2.sort()
  return [s[2] for s in seq2]

def sort_by_attr_inplace(seq,attr):
  """stably sort by an attribute in place"""
  seq[:] = sort_by_attr(seq,attr)

def sort_by_attrs(seq,attrs):
  """sort by a few attributes"""
  import copy
  seq2 = copy.copy(seq)
  attrs.reverse()
  for attr in attrs:
    seq2 = sort_by_attr(seq2,attr)

 return seq2

def sort_by_attrs_inplace(seq,attrs):
  """sort by a few attributes in place"""
  attrs.reverse()
  for attr in attrs:
    seq[:] = sort_by_attr(seq,attr)


def print_all_attrs(obj_instance):
  attrs = dir(obj_instance)
  for attr in attrs:
    if attr[:2] == '__':
       continue
    print attr, getattr(obj_instance,attr)

Innocentive

This seems like an efficient way to do science. Makes sense in a free-market kind of way. Here is the accompanying Scientist article (Stanford accessible only).

Stanford informatics in South Africa

Here is a short article on Stanford's informatics collaboration in South Africa. You can use no@no.com to view genomeweb articles.

for sale: blog

Anyone want to buy the bmi students blog? It's cheap at half the price.

best papers of 2004

My friend sent me a list of papers, voted best of the year by his lab.
Read more


Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV,
Kondrashov AS, Sunyaev S. A universal trend of amino acid gain and
loss in protein evolution. Nature. 2005 Feb 10;433(7026):633-8. Epub
2005 Jan 1 abstract

here

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen
JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH,
Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R,
Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental
genome shotgun sequencing of the Sargasso Sea. Science. 2004 Apr
2;304(5667):66-74. Epub 2004 Mar 4. abstract
here

Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL,
Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global
identification of human transcribed sequences with genome tiling
arrays. Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.
abstract
here

Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M.
Nucleolar proteome dynamics. Nature. 2005 Jan 6;433(7021):77-83.
abstract
here

Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. JASPAR:
an open-access database for eukaryotic transcription factor binding
profiles. Nucleic Acids Res. 2004 Jan 1;32(Database issue)D91-4.
abstract
here

Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau
AY, Walter JC, LaBaer J. Self-assembling protein microarrays.
Science. 2004 Jul 2;305(5680):86-90. abstract
here

Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith
SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W,
Edwards YJ, Cooke JE, Elgar G. Highly conserved non-coding sequences
are associated with vertebrate development. PLoS Biol. 2005
Jan;3(1):e7. Epub 2004 Nov 1 abstract
here

Gerber AP, Herschlag D, Brown PO. Extensive association of
functionally and cytotopically related mRNAs with Puf family
RNA-binding proteins in yeast. PLoS Biol. 2004 Mar;2(3):E79. Epub
2004 Mar 16. abstract
here

Brown P, Sutikna T, Morwood MJ, Soejono RP, Jatmiko, Saptomo EW, Due
RA. A new small-bodied hominin from the Late Pleistocene of Flores,
Indonesia. Nature. 2004 Oct 28;431(7012):1055-61 abstract
here

Wang C, Lefkowitz EJ. SS-Wrapper: a package of wrapper applications
for similarity searches on Linux clusters. BMC Bioinformatics. 2004
Oct 28;5(1):171. abstract
here

Dwyer MA, Looger LL, Hellinga HW. Computational design of a
biologically active enzyme. Science. 2004 Jun 25;304(5679):1967-71.
abstract
here

Aharoni A, Gaidukov L, Khersonsky O, McQ Gould S, Roodveldt C,
Tawfik DS. The 'evolvability' of promiscuous protein functions. Nat
Genet. 2005 Jan;37(1):73-6. Epub 2004 Nov 28 abstract
here

Segal E, Friedman N, Koller D, Regev A. A module map showing
conditional activity of expression modules in cancer. Nat Genet.
2004 Oct;36(10):1090-8. Epub 2004 Sep 26. abstract
here

Park JW, Parisky K, Celotto AM, Reenan RA, Graveley BR.
Identification of alternative splicing eegulators by RNA
interference in Drosophila. Proc Natl Acad Sci U S A. 2004 Nov
9;101(45):15974-9. Epub 004 Oct 18. abstract
here

Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola
B, Suzan M, Claverie JM. The 1.2-megabase genome sequence of
Mimivirus. Science. 2004 Nov 19;306(5700):1344-50. Epub 2004 Oct 14.
abstract
here

King RD, Whelan KE, Jones FM, Reiser PG, Bryant CH, Muggleton SH,
Kell DB, Oliver SG. Functional genomic hypothesis generation and
experimentation by a robot scientist. Nature. 2004 Jan
5;427(6971):247-52. abstract
here