Cavalcade of Mammals

I checked my blog, and found out that WordPress had lost PHP.

Turns out as part of the Mysql upgrade to version 5 I had to uninstall php-mysql.
No binary or package of php-mysql for Mysql version 5 is available so I had to
compile it myself. It took awhile, here’s how it went:

The php module of Apache (httpd) incorporates mysql connection support. It is
built as part of the php build process. So I download php-5.0.4
(PHP).

Building the php webserver module requires the Apache source. I *really*
don’t want to totally build and replace my webserver, there are too many ways
to screw it up. So I’ll just build it, and use the build for making the php
module, but not replace my working web server with the new build.
Find out what version of Apache is installed:
&gr;rpm -qa | grep http
httpd-devel-2.0.51-2.7
httpd-2.0.51-2.7
system-config-httpd-1.2.0-3
httpd-manual-2.0.51-2.7

So find and download the httpd-2.0.51 source from the old version site,
old Apache
untar it, and build it:

./configure --enable-so --enable-cache --enable-cgi
--enable-rewrite=shared --enable-vhost-alias --enable-module=headers
--enable-module=perl --enable-module=log_agent --enable-module=log_referer
--enable-module=include
make
make install

Since I won’t use this build, the exact options aren’t critical. This installs it in the default location, /usr/local/apache2. My old version is still the active one though.

Now go to PHP, untar and build it.

./configure --enable-force-cgi-redirect --with-apxs2 --with-mysql=/usr
make
make install

I had to play around with the configure parameters and still got build errors:
----------------
/usr/bin/ld: /usr/lib64/mysql/libmysqlclient.a(libmysql.o): relocation
R_X86_64_32 can not be used when making a shared object; recompile with -fPIC
/usr/lib64/mysql/libmysqlclient.a(libmysql.o): could not read symbols: Bad
value
----------------

Looking around the web, it looks like php can’t find the shared mysql library.
I look at mysql:

ls -l /usr/lib64/*mysql*

and see a shared library in /usr/lib64 and a static one in /usr/lib64/mysql.
PHP is trying to use the /usr/lib64/mysql one instead of the /usr/lib64 one.
To fix this, I edit the Makefile, replace occurances of /usr/lib64/mysql with
/usr/lib64. Then ‘make clean’, ‘make’. Now it compiles fine.
Do ‘make install’.
It puts the Apache module in /usr/local/apache2/modules. Copy it to my module
dir:

cp /usr/local/apache2/modules/libphp5.so /etc/httpd/modules

Check that /etc/httpd/conf.d/php.conf points to it:
LoadModule php5_module modules/libphp5.so

restart the web server:

/etc/rc.d/init.d/httpd restart

and WordPress is back online!

Numbers of hominid fossils, from Talk Origins

Lubenow (1992) found that there were fossils from almost 4,000 hominid individuals catalogued as of 1976. As of 1999, there were fossils of about 150 Homo erectus individuals, 90 Australopithecus robustus, 150 Australopithecus afarensis, 500 Neanderthals, and more (Handprint 1999). Foley (2004) lists some of the more prominent fossils.

Pretty cool. What species are the other 3,000+ fossils? Some are not classified precisely, I expect, being too fragmentary or just not studied in detail.

My youngest brother has been reading “healthy eating” books, and was telling me that wild animals don’t get cancer. He wasn’t content with my correction and wanted some evidence. Fair enough. Looking around online, I found a few references and was reminded of the Laetrile nonsense.

Laetrile was a quack cancer cure popular in the 70’s. The tout was that sharks don’t get cancer, and that taking pills made from ground up shark cartilage would cure cancer. This paragraph give a summary of the Laetrile cure fad:

Crude shark cartilage extract is not a cure for cancer in humans
Promotion of cartilage extracts from sharks has had two negative outcomes: a decline in shark populations, and a diversion of patients from effective cancer treatment. The argument has been that sharks don’t get cancer. However, both malignant and benign neoplasms of sharks and their relatives were described by Gary Ostrander and associates at Johns Hopkins University (Maryland), Penn State College of Medicine, and Registry of Tumors in Lower Animals (Virginia). So far there is no evidence to support the use of crude cartilage nor any cartilage extract to reach and eradicate cancer cells. The authors see the use of shark cartilage extracts as another example of pseudoscience used in decision making where the facts are not considered. (Cancer Research 64: 8485-8491, 2004)

The reference to the Registry of Tumors in Lower Animals sounds intriguing so I looked it up. The collection is searchable online after registering, and I’ve included a link. The Registry includes many cases of cancer in wild animals.

Looking around a bit more, I find someone else has considerately done a search of the literature, and posted abstracts. I’ve includes them below (lost track of the original source). These reports come from journals indexed by Pubmed which indexes biomedical journals, so papers in ecological or field biology journals would be missed. As you can see, there are many reports describing cancer in wild animals. The list is long, but skimming shows that tumors in wild animals have been observed many times.

Next up, I’ll look into the notion you’ve gotten that microwaving your food makes it dangerous to eat.

Cesk Patol 1996 May;32(2):78-83

[Tumors in wildlife].

[Article in Czech]

Karpenko A, Bukovjan K.

Oddeleni patologie SZZ, Benesov u Prahy.

Wild animal tumours have not been much studied yet. Authors found six
mostly benign cases in Czech Republic in checking hunts between the years
1988 and 1993: Mature differentiated ovarian teratoma and apocrine skin
adenoma in field hare, intraductal mammary papillomatosis in a roe,
complex odontoma and pleomorphic mammary carcinoma (single malignancy in
the group) in fox. A soft tissue tumour in a fallow-buck’s neck could not
be histogenetically classified. A high structural equivalence of animal
and human tumours allows using ICD-O classification as a whole.

PMID: 9560906 [PubMed – indexed for MEDLINE]

J Vet Med Sci 1997 Aug;59(8):703-6

Spontaneous gastric carcinoid tumors in the striped field mouse (Apodemus
agrarius).

Oh SW, Chae C, Jang D.

Department of Veterinary Pathology, College of Veterinary Medicine, Seoul
National University, Suwon, Kyounggi-Do, Republic of Korea.

Gastric carcinoid tumors were found in seven of 135 striped field mice
(Apodemus agrarius) by routine histopathologic examination. All these
carcinoids occurred in mature striped field mice aged 72-100 weeks. Six
animals were females and only one was male. Only two of seven tumors were
detectable by gross examination. Grossly, tumors were located in the
fundus of the glandular stomach. All seven tumors were microscopically
single in the stomach and two mice exhibited extragastric metastasis.
Tumors from all the mice were characterized by densely packed sheets of
round to polygonal cells, subdivided into packets by a fine fibrovascular
stroma. The cytoplasm of all tumor cells from all the mice contained
argyrophil granules when stained by Grimelius and Sevier-Munger silver
procedures. All seven mice with gastric carcinoids exhibited positive
immunoreactivity to neuron specific enolase. Psammoma bodies,
concentrically laminated microcalcification, were characteristic findings
in gastric carcinoids from five mice. There were also a concomitant and
independent hepatocellular adenoma in one case and hepatocellular
carcinoma in two cases. The present cases provide the first description
of spontaneous gastric carcinoid tumors in the striped field mice.

PMID: 9300368 [PubMed – indexed for MEDLINE]

Leukemia 1997 Apr;11 Suppl 3:170-1

Plasmacytoid leukemia of chinook salmon.

Kent ML, Eaton WD, Casey JW.

Department of Fisheries and Oceans, Pacific Biological Station, Nanaimo,
B.C., Canada.

Plasmacytoid leukemia is a common disease of seawater pen-reared chinook
salmon (Oncorhynchus tshawytscha) in British Columbia, Canada, but has
also been detected in wild salmon, in freshwater-reared salmon in United
States, and in salmon from netpens in Chile. The disease can be
transmitted under laboratory conditions, and is associated with a
retrovirus, the salmon leukemia virus. However, the proliferating
plasmablasts are often infected with the microsporean Enterocytozoon
salmonis, which may be an important co-factor in the disease.

PMID: 9209333 [PubMed – indexed for MEDLINE]

Pathol Int 1996 Dec;46(12):919-32

Mouse mammary tumor virus and mammary tumorigenesis in wild mice.

Imai S.

Nara Prefectural Institute of Public Health, Japan.

The current knowledge of the distribution of the mouse mammary tumor
virus (MMTV) proviral genomes and the mechanism of mammary tumorigenesis
by MMTV in mice, with the main emphasis on Asian feral mice, is reviewed.
The relevant earlier discoveries on the mode of MMTV transmission are
summarized to provide an outline of the biology of MMTV. Finally, the
viral etiology of human breast cancer will be discussed.

Publication Types:
Review
Review, academic

PMID: 9110343 [PubMed – indexed for MEDLINE]

Adv Neurol 1991;56:473-9

Retroviral leukemia and lower motor neuron disease in wild mice: natural
history, pathogenesis, and genetic resistance.

Gardner MB.

Department of Pathology, School of Medicine, University of California, Davis
95616.

Publication Types:
Review
Review, tutorial

PMID: 1649545 [PubMed – indexed for MEDLINE]

J Wildl Dis 1985 Oct;21(4):386-90

Diseases diagnosed in wild turkeys (Meleagris gallopavo) of the southeastern
United States.

Davidson WR, Nettles VF, Couvillion CE, Howerth EW.

Diagnostic findings are presented on 139 sick or dead wild turkeys
examined during the period 1972 through 1984. Turkeys originated from
eight southeastern states (Alabama, Arkansas, Florida, Georgia, South
Carolina, Tennessee, Virginia, West Virginia) and included 31 turkeys
categorized as capture-related mortalities and 108 turkeys categorized as
natural mortalities. Frequent diagnoses (greater than or equal to 10% of
case accessions) in the natural mortality group were trauma, avian pox,
and histomoniasis. Less frequent diagnoses (less than or equal to 4% of
case accessions) included malnutrition/environmental stress syndrome,
coligranuloma-like condition, crop impaction, bumblefoot, organophosphate
toxicosis, infectious sinusitis, a lympho-proliferative disease,
salmonellosis, aspergillosis, toxoplasmosis, crop trichomoniasis, and
melorheostosis.

PMID: 4078973 [PubMed – indexed for MEDLINE]

Acta Vet Scand 1985;26(1):61-71

Leukaemic neoplasia in free-living mammals in Denmark.

Elvestad K, Henriques UV.

PMID: 3839967 [PubMed – indexed for MEDLINE]

Int J Cancer 1981 Aug 15;28(2):241-7

Natural killer cell activity in a population of leukemia-prone wild mice
(Mus musculus).

Scott JL, Pal BK, Rasheed S, Gardner MB.

Natural cell-mediated cytotoxicity against YAC-I targets was measured in
splenocytes from leukemia-prone wild mice trapped near Lake Casitas (LC)
in southern California. Cytotoxicity was mediated by cells that were
non-adherent to nylon wool, non-phagocytic and resistant to thy-1.2
antiserum plus complement. Natural MuLV viremia in LC mice did not impair
splenic cytotoxicity against TAC-I target cells, Cells infected with
amphotropic and ecotropic MuLV of wild mouse origin were not appreciably
lysed by LC splenic effectors. Although variable levels of cytotoxicity
were detected against TAC-1 by normal spleen cells, consistently low
levels of cytotoxicity against allogenic LC lymphoma, sarcoma and
carcinoma targets were found using the same splenocytes. These results
indicate that LC mice possess splenocytes with the characteristics of
natural killer (NK) cells as defined in inbred mice. The resistance of
LC-derived targets to lysis by LC NK cells suggests that NK cells may not
be involved in natural tumor immunosurveillance or that the development
of spontaneous tumors may involve escape from NK-mediated effector
mechanisms.

PMID: 6274813 [PubMed – indexed for MEDLINE]

Vet Pathol 1977 Nov;14(6):539-46

Gynecologic pathology in the rhesus monkey (Macaca mulatta). II. Findings in
laboratory and free-ranging monkeys.

DiGiacomo RF.

The most prevalent findings in reproductive tracts of 38 laboratory and
17 free-ranging Rhesus female monkeys were vaginitis, cervicitis,
metritis, pelvic endometriosis and uterine adenomyosis. Several monkeys
had cervical dysplasia and one had a serous cystadenoma. The findings in
the two groups were similar although prevalence for several diseases
differed. There was a significant relationship between the occurrence of
vaginitis, metritis, adenomyosis and endometriosis and gravidity, time
since last pregnancy, number of matings, hysterotomies, reproductive
ability and reproductive status.

PMID: 412291 [PubMed – indexed for MEDLINE]

J Wildl Dis 1999 Oct;35(4):804-7

Relating tumor score to hematology in green turtles with
fibropapillomatosis in Hawaii.

Work TM, Balazs GH.

U.S. Geological Survey, Biological Resource Division, National Wildlife
Health Center, Honolulu Field Station, Hawaii 96850, USA.
thierry_work@usgs.gov

The relationship between hematologic status and severity of tumor
affliction in green turtles (Chelonia mydas) with fibropapillomatosis
(FP) was examined. During 1 wk periods in July 1997 and July 1998, we
bled 108 free-ranging green turtles from Pala’au (Molokai, Hawaii, USA)
where FP is endemic. Blood was analyzed for hematocrit, estimated total
solids, total white blood cell (WBC) count and differential WBC count.
Each turtle was assigned a subjective tumor score ranging from 0 (no
visible external tumors) to 3 (heavily tumored) that indicated the
severity of FP. There was a progressive increase in monocytes and a
decrease in all other hematologic parameters except heterophils and total
numbers of white blood cells as tumor score increased. These data
indicate that tumor score can relate to physiologic status of green
turtles afflicted with FP, and that tumor score is a useful field monitor
of severity of FP in this species.

PMID: 10574546 [PubMed – indexed for MEDLINE]

J Wildl Dis 1999 Oct;35(4):753-62

Descriptive epidemiology of roe deer mortality in Sweden.

Aguirre AA, Brojer C, Morner T.

Department of Wildlife, The National Veterinary Institute, Uppsala, Sweden.
aguirre@wpti.org

A retrospective epidemiologic study was conducted to examine causes of
mortality of 985 wild roe deer (Capreolus capreolus) submitted to the
National Veterinary Institute (SVA; Uppsala, Sweden) from January 1986 to
December 1995. Age, sex, body condition, and geographic distribution as
related to disease conditions are reported herein. The most common causes
of mortality in roe deer were trauma (19%), winter starvation (18%),
gastritis/enteritis (15%), bacterial infections (11%), parasitic
infection (11%), systemic diseases (11%), neoplasia (2%), congenital
disorders (1%), and miscellaneous causes (6%). Cause of death was not
determined in 6% of the cases. The distribution of causes of death
reported in this study differ from previous works in Sweden in that
infectious and parasitic diseases were more common than winter
starvation. The pathologic findings in studies like this do not
necessarily represent what is occurring in the natural environment, but
they do provide a good indication of distribution of diseases over time
as well as age and sex structure in relation to disease conditions.
Further research and more detailed studies are in progress to better
understand specific mortality factors as well as etiologies of certain
described diseases in roe deer in Sweden.

PMID: 10574535 [PubMed – indexed for MEDLINE]

J Zoo Wildl Med 1999 Mar;30(1):165-9

Herpesvirus-associated papillomas in koi carp (Cyprinus carpio).

Calle PP, McNamara T, Kress Y.

Wildlife Health Sciences, Wildlife Conservation Society, Bronx, New York
10460-1099, USA.

From January through November 1994, 32% (7/22) of koi carp (Cyprinus
carpio) maintained in indoor aquariums developed proliferative cutaneous
lesions that consisted of single to multiple 2-10-mm whitish to pink
fleshy masses usually associated with fin rays. Although scaleless koi
were more commonly affected (3/6) than were normally scaled koi (4/16),
the difference in incidence rates was not significant (chi2 text, P >
0.05). Lesions typically resolved spontaneously in 1-3 wk, occasionally
persisted for >3 mo, and recurred in several fish after 2-5 mo. Fish were
otherwise asymptomatic. Wet mount preparations from lesions were densely
cellular and consisted of hyperplastic epidermal cells of normal
morphology without parasites or inflammatory cells. Histologically,
biopsies were consistent with papillomas and were characterized by a
marked benign epidermal hyperplasia without inclusion bodies or
inflammatory infiltrate. Transmission electron microscopic examination
revealed intranuclear and intracytoplasmic herpesvirus virions. Virus
isolation attempts were unsuccessful.

PMID: 10367660 [PubMed – indexed for MEDLINE]

J Wildl Dis 1999 Apr;35(2):392-4

Adenocarcinoma of the mammary gland in a red fox from Austria.

Janovsky M, Steineck T.

Research Institute of Wildlife Ecology, University of Veterinary Medicine,
Vienna, Austria.

A mammary gland adenocarcinoma was diagnosed in an adult red fox (Vulpes
vulpes) which was shot in Austria in August 1995. Metastases were found
in the kidneys and liver. This is the first reported case of an
adenocarcinoma in a fox, and lack of mammary gland carcinoma in this
species may be age related.

PMID: 10231770 [PubMed – indexed for MEDLINE]

This turned out to be pretty straightforward once I got the order of steps right. Don’t make the filesystems before the mkraid, you will end up with “bad superblock” errors later.

I added two 400Gb SATA hard drives in RAID1 to an existing system. I already had one pair of drives in RAID 1, the new drives form a new RAID array.

1) Phyiscally add the drives.

2) Run fdisk, make one partition on each drive.
fdisk /dev/hdc
fdisk /dev/hdd

3) Edit /etc/raidtab, add section for /dev/md1:
raiddev /dev/md1
raid-level 1
nr-raid-disks 2
chunk-size 256
persistent-superblock 1
nr-spare-disks 0
device /dev/sdc1
raid-disk 0
device /dev/sdd1
raid-disk 1

4) Make RAID, needed ‘force’ flag:
mkraid -f /dev/md1
mkraid -R /dev/md1

5) Make filesystems:
mke2fs -j /dev/sdc1
mke2fs -j /dev/sdd1

This takes 10 min or so.

6) Add new filesystem to /etc/fstab for automounting:
/dev/md1 /home ext3 defaults 1 2

And now the keychain drive gets pushed from sdc to sde:
/udev/sde1 /mnt/key vfat owner,kudzu 0 0

7) Mount new RAID:
mkdir /data
mount /data

Useful RAID commands:
more /proc/mdstat
mdadm -D /dev/md1

Useful guide:
Software-RAID-HOWTO

tried running the Graphviz programs on OS X (sudo fink install graphviz) and got a font error message, ‘Could not find/open font : Times in…’

To use the Graphviz programs with OS X, need to specify

-Nfontname=luxisr

The program can use fonts in /usr/X11R6/lib/X11/fonts/TTF. This is part of
the Apple supplied X11 (part of the optional/developer OS install disk? I don’t recall when/how I installed it.).
Found this info at: link

I heard an assertion nanobacteria exist along with some speculation about them and so on. It was news to me and got me wondering if I had missed a discovery announcement, so I ran some numbers:

Consider a large nanobacteria, 30 nm by 100 nm. It has an approximate volume of 7e-23 m³.

How much DNA could this volume contain? Pop up a DNA molecule in Chime and get an estimate of dimensions: 20 bp run for 6.4 nm, so 0.32 nm / bp. The double helix has a radius of 1.3 nm.

Length of DNA with a volume equal to the cell = 7e-23 m³ / [ (1.3 nm)² x Ï€ ] = 1.3e-5 m
Bps = length / bp length = 1.3e-5 m / 0.32 nm = 42 kb of DNA.

A low average bacterial gene length is 300 bp, so a nanobacteria could hold a maximum of 42 kb / 300 bp = 139 genes. The minimum number of genes for an independent living organism is 300 – 500, so a nanobacteria can’t have enough genes. It can’t exist. But let’s run the other numbers, on proteins.

A typical protein is 3 nm, lets call it a cube with a volume of (3 nm)3 = 2.7e-26m³.
A nanobacteria can hold 7e-23m³ / 2.7e-26m³ = 2600 proteins total. Low but not a hard limit on existence.

Now let’s put this together and describe a nanobacteria. 30% of the volume is water and small molecules. Of the remainder, let’s say 2/3 is DNA and 1/3 is protein. The nanobacteria contains enough DNA for 65 genes, and 600 proteins. Which means nanobacteria can’t exist, they are too small. There are quite a few unlikely bits in biology (pretty much every rule in biology has exceptions), so I’ll qualify it and say it is quite unlikely that nanobacteria exist. And to my estimates, add the evidence from projects to mass sequence DNA extracted from the environmental samples–if nanobacteria exist, their DNA would turn up in these projects, and no new phylum of sequences has emerged.

An E. coli by contrast is 1 µ x 3 µ and can hold 600 Mb of DNA and 20 million proteins. It’s genome is actually 4.6 Mb, and the extra space is taken up by a cell wall and protein.

Upgraded the kernel on my linux server and it was the easiest thing ever:

yum upgrade kernel-smp

It updated grub and everything! Color me surprised. Linux is getting *so* easy to use.

Have a look at this octopus. It camoflages itself while it walks around.

Two tiny species of tropical octopus have demonstrated a remarkable disappearing trick. They adopt a two-armed ‘walk’ that frees up their remaining six limbs to camouflage them as they slink away from trouble.

View movies below the fold.
Read the rest of this entry »

From an interview with National Center for Atmospheric Research in Colorado’s Gerald Meehl discussing an NCAR paper in Science:

Experts say sea levels have risen 4 inches already over the past century and could rise between 4 and 40 inches more in the next century.

If completely melted, the Greenland ice sheet would add 25 feet to overall sea level and the West Antarctic Ice Sheet would raise it by 16 feet — enough to swamp most of Florida, Bangladesh and New York City’s Manhattan island.

So that’s the upper limit on sea level rise. And while the modelers predict a mm/year rate, ice sheets melt catastrophically and we’re getting into the range of losing some of them, so I’ll make a wild-ass guess that we’ll see a bad decade with a foot or so sea level rise this century.

(To digress, this reminds me of how bad the premise of Waterworld is. You know a movie’s science is bad when it makes you look fondly on the scientific plausibility of Planet of the Apes. Waterworld is a full point higher on the Scientfic Implausibility Richter scale.)

From the abstract of the paper, “The Climate Change Commitment”. Wigley, TML. (2005) Science 307:1766-9:

These constant-composition (CC) commitments and their uncertainties are quantified. Constant-emissions (CE) commitments are also considered. The CC warming commitment could exceed 1°C. The CE warming commitment is 2° to 6°C by the year 2400. For sea level rise, the CC commitment is 10 centimeters per century (extreme range approximately 1 to 30 centimeters per century) and the CE commitment is 25 centimeters per century (7 to 50 centimeters per century).

The CE senario predicts 2.5 mm/year rise, but emissions are rising so this is definitely an underestimate.

Notes on some bioinformatics books from two perspectives. Here’s what I’m looking for: 1) advanced discussion of computational and statistical methods for genomics, especially microarray analysis, and 2) suitability for an intro and survey bioinformatics course I teach.

THE ANALYSIS OF GENE EXPRESSION DATA: METHODS AND SOFTWARE
edited by Giovanni Parmigiani, Elizabeth S Garrett, Rafael A Irizarry, Scott L Zeger
companion website
Great medium depth howto. Covers R, dChip, SAM, and packages that take more sophisticated approaches to analysis, clustering, and visualization.

Bioinformatics for Geneticists
Edited by Michael R. Barnes and Ian C. Gray
Published Online: 22 May 2003
Genomic orientation, but too light and introductory for my needs, too genomic focused for my course. Good starting point book for a geneticist.

Advances in Systems Biology
Series: Advances in Experimental Medicine and Biology, Vol. 547
Opresko, Lee K.; Gephart, Julie M.; Mann, Michaela B. (Eds.)
2004
Pulled this book for A Systems Approach to Discovering Signaling and Regulatory Pathways—or how to digest large interaction networks into relevant pieces by Trey Ideker.

Microarray Gene Expression Data Analysis: A Beginners Guide
by Helen C. Causton , John Quackenbush , Alvis Brazma
2003
What it says it is: design, image processing, normalization, basic stats, clustering.

Bioinformatics: Databases and Systems
Edited by Stan Letovsky
Kluwer Academic Press, Boston, 1999
A chapter a database. Covers the usual gang, plus chapters on WIT/WIT2, KEGG, BioWidgets (Java), and AceDB (overview).

Statistical Methods in Bioinformatics An Introduction
Series: Statistics for Biology and Health
Ewens, Warren J. and Grant, Gregory
2nd ed. , 2004, 588p
errata
Heavy statistical treatment of sequence analysis. Starts with stats, then stat properties of one seq, multiple seq alignments, BLAST, Marlov chains, HMMs.

‘In Silico’ Simulation of Biological Processes
No. 247 Novartis Foundation Symposium
270 pages January 2003
Picked this up for the GO chapter. Also has a chapter on KEGG.

Micr
oarrays Methods and Applications: Nuts and Bolts
Edited by Gary Hardiman
2003
Covers topics from basic MA howtos to more specialized applications. A mixed bag. One chapter on microarray scanner evaluation, another on C. elegans 50-mer oligos made by the Hardiman lab at UCSD. Chapter text and figures are online.

Microarray Quality Control
by Wei Zhang, Ilya Shmulevich and Jaakko Astola
136 pages February 2004
What the title says. Microarrays from a core facility perspective. Ends with normatization. Covers long oligo design.

Microarray Bioinformatics
by Dov Stekel
Cambridge University Press. 2003
Thorough and clear coverage of microarray design, construction, image proc, and normalization. What caught my eye was the chapter on oilgo design, but its all good. Best single book on microarrays I’ve seen.

Bioinformatics: Methods and Protocols
Edited by Stephen Misener, Stephen A. Krawetz
Humana Press; 1st edition 2000
Program based by chapter. Too program based for a course. Has good chpaters on Clustal and Phylip. A chapter on Trascription control regions using MatInspector/GenomeInspector, weight matrix based sequence scanning for single or paired binding sites.

Computational Molecular Biology: an Algorithmic Approach
by Pavel A. Pevzner
MIT Press, 2000
Takes a unique approach. Looks at interesting computational aspects of seqeunce-based biology, and sometimes takes an odd sideways view of problems, getting deep into the underlying mathematics. A great complement to a more straightforward survey book. The topic coverage isn’t broad enough for my course, and the topics get covered in more depth than I need. Runs thorugh algorithmics of restircition digests to microarrays including, of course, sequencing by hybridization. Covers algorithmics of genomic comparisons. Great source book for a serious comp bio student.

DNA Microarrays: A Practical Approach
Edited by Mark Schena
Oxford University Press, Oxford, UK, 1999
A book on microarray technology. From DNA spotted on glass to enzymatic oligo arrays to ink jets, to microelectronic arrays. Written early on when many different approaches were being explored. Great source for technical information.

Mathematics of Genome Analysis
by Jerome K. Percus
Cambridge University Press; 1st edition 2002
Not a genomics book, but a mathmatician’ s look at DNA sequence, from clone libraries through seq alignments.

Post-genome Informatics
by Minoru Kanehisa
Oxford University Press, Oxford, 2000
Cool cover! Written by the guy behind KEGG. An eclectic choice of topics, first databases, then sequence analysis basics, then network analysis. Had a few pages on comparing networks that I found useful.

Guide to Analysis of DNA Microarray Data
by Steen Knudsen
John Wiley and Sons, New York, 2002
A what-to-do book on microarray data analysis. Very short, too short to explain how to do things, but describes what to do, issues to consider, and what results will look like. Useful as a place to start, will show you what you don’t know. The linked site has example R and BioConductor code.

Methods of Microarray Data Analysis II
Edited by Simon M. Lin and Kimberly F. Johnson
Springer, 2002
Papers from CAMDA ‘01 Various array analysis, especially advanced clsutering methods. Particularly interesting are:

• Biology-Driven Clustering of Microarray Data; K.R. Coombes, et al.
  GO-based clustering.
• Analysis of Gene Expression Profiles and Drug Activity Patterns by Clustering and Bayesian Network Learning; Jeong-Ho Chang, et al.
• Topomap and bayesian clustering

DNA Arrays: Technologies and Experimental Strategies
Edited by Elena V. Grigorenko
CRC Press, 2001
What caught my eye are the technology chapters, one on oligo arrays and another on electrochemical array detection.

DNA Arrays: Methods and Protocols
Edited by Jang B. Rampal
Humana Press, 2001
This is another array technology book. Great information on ink-jet and photolithographic oligo synthesis. There are several sequencing by hybridization articles. It starts with a chapter on the history of the field by Southern. Great book for a collection of articles!