Blog Archive 2

Bioinformaticist or Bioinformatician?

Why are there two words for a bioinformatics scientist, bioinformaticist and bioinformatician? Is there a difference between them?

In 1993, when I was hired in my first industry job as what we would now call a bioinformaticist or bioinformatician, I hadn’t heard of either term. When I was asked what I thought my job title should be, I answered computational molecular biologist. I chose that title to recognize my training in molecular biology and my acquired computer skills.

But by 1995, the terms bioinformatics and bioinformaticist had gained widespread recognition. Now, in 2006, it is my impression that the term bioinformatician is more popular than bioinformaticist, and I have bioinformatician on my business card.

The CD-ROM edition of the American Heritage Dictionary, 4th Edition, makes it easy to find all words in the dictionary with the same suffix. For example, I searched the CD-ROM for all words matching the pattern *icist or *ician, where the asterisk is the standard wild card character that matches any number of characters.

The Suffix -ician

In this dictionary, the suffix -ician is defined as “one who practices; a specialist”.

Here are the 45 words that end in -ician that carry this meaning:

Note: The following words, although they end in -ician, don’t carry the meaning of one who is a specialist or expert: academician, Cilician, Galician, Ordovician, patrician, and Phoenician.

The Suffix -icist

The suffix -icist derives from three suffixes, -ic, -s, and -ist. The combined suffix carries the meaning of one who is a specialist or expert in a science or art. Here are the 39 words in the American Heritage Dictionary, 4th Edition, that carry this meaning:

Note: The following words, although they end in -icist, are derived from words that end in -ism and do not carry the meaning of one who is a specialist or expert: apocalypticist, atlanticist, ecumenicist, organicist, and pacificist.

No Conclusion

The words I identify with in these lists are mathematician and statistician, two -ician words. (I also identify with biologist, chemist, and programmer, but these don’t fall into the two categories I’m examining here.)

Other than that, I use the two words interchangeably. Most people have never heard these words, and it’s a pain to have to spell them out, at which point I just say that I'm a scientist.

27-May-2006 | permalink

New Perl Books

I have added two books on Perl to my want list.

The first is Higher Order Perl: Transforming Programs with Programs, by Mark Jason Dominus. This book, which was published in March, 2005, teaches people like me, who are trained in the procedural paradigm of C-like programming languages, how to use functional programming techniques characteristic of LISP.

The second book is Perl Testing: A Developer’s Notebook, by Ian Langworth and chromatic. This O’Reilly book, published in July, 2005, provides a short guide on how to use Perl’s test suites. I need to learn how to do this for my job.

I am in the middle of reading Intermediate Perl by Randal L. Schwartz, brian d foy, and Tom Phoenix. (I hope to provide a complete review soon.) When I finish, I’ll probably pick up one of these two other Perl books.

I provide brief reviews of other Perl books I have read in the Perl section of my Bioinformatician’s Bookshelf.

25-May-2006 | permalink

Naming Computers for Protein Scientists

Research groups and companies often need to come up with names for many computers. Some systems I have seen are:

• characters from The Hobbit and The Lord of the Rings, by J. R. R. Tolkien (e.g., Bilbo, Frodo, Balin, Thorin, Gandalf)
• names of gods and goddesses (e.g., Zeus, Hera, Aphrodite, Hermes)
• names of ancient cities (e.g., Babylon, Rome, Athens, Carthage)
• names of elements (e.g., cobalt, helium, oxygen, uranium)
• names of biologists (e.g., Darwin, Franklin, Crick, Watson, Sanger)

I work in a protein-oriented group. In case I have the opportunity of naming computers in my group, I have compiled a list of names of protein scientists. Each of the researchers in the table below was awarded the Nobel Prize in Chemistry or in Physiology or Medicine for research on proteins. In the table, I give the name of the scientist, the name of the prize, the year the prize was awarded, and the brief description of the research that was being recognized by the prize.

Scientist	Prize	Year	Awarded For
Agre	Chemistry	2003	“the discovery of water channels” in cell membranes
Anfinsen	Chemistry	1972	“work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active confirmation”
Arber	Physiology or Medicine	1978	(with Nathans and Smith) “the discovery of restriction enzymes and their application to problems of molecular genetics”
Blobel	Physiology or Medicine	1999	“the discovery that proteins have intrinsic signals that govern their transport and localization in the cell”
Boyer	Chemistry	1997	(with Walker) “the elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)”
Deisenhofer	Chemistry	1988	(with Huber and Michel) “the determination of the three-dimensional structure of a photosynthetic reaction center”
Edelman	Physiology or Medicine	1972	(with Porter) “their discoveries concerning the chemical structure of antibodies”
Fenn	Chemistry	2002	(with Tanaka) “their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules”
Fischer	Physiology or Medicine	1992	(with Krebs) “their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism”
Gilman	Physiology or Medicine	1988	(with Rodbell) “their discovery of G-proteins and the role of these proteins in signal transduction in cells”
Guillemin	Physiology or Medicine	1977	(with Schally) “their discoveries concerning the peptide hormone production of the brain”
Huber	Chemistry	1988	(with Deisenhofer and Michel) “the determination of the three-dimensional structure of a photosynthetic reaction center”
Kendrew	Chemistry	1962	(with Perutz) “their studies of the structures of globular proteins”
Kornberg	Physiology or Medicine	1959	(with Ochoa) “their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid”
Krebs	Physiology or Medicine	1992	(with Fischer) “their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism”
MacKinnon	Chemistry	2003	“structural and mechanistic studies of ion channels” in cell membranes
Merrifield	Chemistry	1984	“his development of methodology for chemical synthesis on a solid matrix”
Michel	Chemistry	1988	(with Deisenhofer and Huber) “the determination of the three-dimensional structure of a photosynthetic reaction center”
Moore	Chemistry	1972	(with Stein) “contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule”
Nathans	Physiology or Medicine	1978	(with Arber and Smith) “the discovery of restriction enzymes and their application to problems of molecular genetics”
Ochoa	Physiology or Medicine	1959	(with Kornberg) “their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid”
Pauling	Chemistry	1954	“research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances”
Perutz	Chemistry	1962	(with Kendrew) “their studies of the structures of globular proteins”
Porter	Physiology or Medicine	1972	(with Edelman) “their discoveries concerning the chemical structure of antibodies”
Prusiner	Physiology or Medicine	1997	“his discovery of prions—a new biological principle of infection”
Rodbell	Physiology or Medicine	1988	(with Gilman) “their discovery of G-proteins and the role of these proteins in signal transduction in cells”
Schally	Physiology or Medicine	1977	(with Guillemen) “their discoveries concerning the peptide hormone production of the brain”
Skou	Chemistry	1997	“the first discovery of an ion-transporting enzyme, Na+, K+-ATPase”
Smith	Physiology or Medicine	1978	(with Arber and Nathans) “the discovery of restriction enzymes and their application to problems of molecular genetics”
Stein	Chemistry	1972	(with Moore) “contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule”
Tanaka	Chemistry	2002	(with Fenn) “their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules”
Theorell	Physiology or Medicine	1955	“discoveries concerning the nature and mode of action of oxidation enzymes”
Tiselius	Chemistry	1948	“his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins”
Walker	Chemistry	1997	(with Boyer) “the elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)”
Wüthrich	Chemistry	2002	“his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution”
Yalow	Physiology or Medicine	1977	“[her] development of radioimmunoassays of peptide hormones”

24-May-2006 | permalink

Better Perl CGI

I have begun a quest to learn a better way to carry out Perl CGI programming. This weekend I began exploring the CGI::Application Perl module, written by Mark Stosberg. I haven’t actually started using it yet, but I’ve been doing a lot of background reading.

Here are some useful links for further reading:

• CGI::Application—Framework for building reusable web-applications
• perl.com: Using CGI::Application
• CGI::Application: A Simple, Extensible Web Framework [CGI & Perl Tutorials]
• CGI::Application—HomePage
• MVC Frameworks in Perl—O’Reilly ONLamp Blog
• Model-view-controller—Wikipedia, the free encyclopedia
• Ovid’s CGI Course

Another module that is useful for managing Perl CGI is HTML::Template. Special hooks are available in CGI::Application to use HTML::Template. For more information, see:

• HTML::Template—Perl module to use HTML templates from CGI scripts
• perl.com: Using CGI::Application
• Introducing HTML::Template [CGI & Perl Tutorials]

An alternative to CGI::Application may be CGI::Prototype by Randal L. Schwartz. A couple of links for further reading are:

• CGI::Prototype
• Prototype Programming for Classless Classes (Feb 04)

A new alternative may be Class::CGI by Curtis “Ovid” Poe. For more information see:

• Class::CGI
• Who the heck is Ovid?—O’Reilly ONLamp Blog

14-May-2006 | permalink

Single Letter Codes

Today at work the following question came up:

What letters are valid in the single letter amino acid code but do not coincide with letters for bases in DNA and mRNA, including ambiguous bases? The context of this question is differentiating between peptide sequences and nucleotide sequences.

I know the single letter amino acid code by heart. I know most of the single-letter base code, but I always get tripped up by which bases are represented by K and M. Here is the table of letters and their meanings:

Letter	Amino Acid	Base
A	Alanine	A
B		C or G or T (not A)
C	Cysteine	C
D	Aspartate	A or G or T (not C)
E	Glutamate
F	Phenylalanine
G	Glycine	G
H	Histidine	A or C or T (not G)
I	Isoleucine
J
K	Lysine	G or T (Keto)
L	Leucine
M	Methionine	A or C (aMino)
N	Asparagine	A or C or G or T (aNy)
O
P	Proline
Q	Glutamine
R	Arginine	A or G (puRine)
S	Serine	C or G (Strong base-pairing)
T	Threonine	T
U	Selenocysteine	U
V	Valine	A or C or G (not T)
W	Tryptophan	A or T (Weak base-pairing)
X
Y	Tyrosine	C or T (pYrimidine)
Z

Examination of this table reveals that the answer to the question is E, F, I, L, P, and Q.

This might be a fun question to use when interviewing a job candidate for a bioinformatics position.

08-May-2006 | permalink

Pod::Usage

I applied for a job that required experience in object-oriented Perl. During the interviews, I was given an oral examination on Perl. One of the questions I couldn’t answer was, “Identify Pod::Usage”.

The correct answer is that Pod::Usage is a Perl module that allows the programmer to use POD (Plain Old Documentation) for creating a usage message when the user doesn’t supply the desired arguments to a script.

I worked out a complete example of the use of Pod::Usage, which I added to my pages on intermediate Perl.

15-Apr-2006 | permalink