BMC Bioinformatics. 2004; 5: 191.
Published online 2004 December 7. doi: 10.1186/1471-2105-5-191.
Copyright © 2004 Chen et al; licensee BioMed Central Ltd.
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information
Yian A Chen,corresponding author1 David J Mckillen,2 Shuyuan Wu,1 Matthew J Jenny,2,3 Robert Chapman,3,4 Paul S Gross,2,3 Gregory W Warr,2,3 and Jonas S Almeida1
1Department of Biostatistics, Bioinformatics, and Epidemiology, Medical University of South Carolina, Charleston, SC, USA
2Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
3Marine Biomedicine and Environmental Science Center, Medical University of South Carolina, Charleston, SC, USA
4South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, SC, USA
corresponding authorCorresponding author.
Yian A Chen: firstname.lastname@example.org; David J Mckillen: email@example.com; Shuyuan Wu: firstname.lastname@example.org; Matthew J Jenny: email@example.com; Robert Chapman: firstname.lastname@example.org; Paul S Gross: email@example.com; Gregory W Warr: firstname.lastname@example.org; Jonas S Almeida: email@example.com
Received August 21, 2004; Accepted December 7, 2004.
In this study, we propose a probe selection procedure for cDNA microarray that tracks both sequence redundancies and functional representativeness of the selected probes in an integrated sequence diversity plot (SDP). SDP includes a sequence diversity index (SDI) to measure the sequence similarities within EST clusters quantitatively. The issue of how many probes are sufficiently representative for all collected ESTs is approached in a manner similar to the choice of dimensions to retain in principle component analysis (PCA). This approach reflects the fact that there is no definitive right answer to the question ; the number of “clusters” of ESTs may vary as the stringency of microarray hybridization condition changes. All collected ESTs are automatically annotated using Gene Ontology  terms, and then a unique probe GO index (UPGI), a functional index, was devised to access functionally how representative the selected probes are. This integrated and flexible method using SDP allows users to decide which clustering method and stringency to use when designing a cDNA microarray for organisms with limited genomic information based on their logistical constraint and experimental purposes. A small data set of ESTs was used to test this algorithm so that the detailed results of this algorithm could be examined.
Accurately Describing a Technology That Does Not Yet Exist
by Mike Treder
The mission of the Center for Responsible Nanotechnology (CRN) is to raise awareness of the issues presented by advanced nanotechnology: the benefits and dangers, and the possibilities for responsible use. We explore the ethical, legal, and social implications (ELSI) of nanotechnology, and its potentially disruptive consequence, exponential general-purpose molecular manufacturing. The purpose of CRN is to educate those who will influence the use of nanotechnology, or be affected by it.
An important aspect of this educational process is to create ‘theoretical, pictorial and textual representations’ of what may become possible through nanoscale science and engineering (NSE), especially though molecular manufacturing. CRN studies, clarifies, and researches the issues involved—political, economic, military, humanitarian, and technological—and presents the results for both technical and popular audiences, working to supply the information as effectively as possible.
Our intention is to provide well-grounded and complete information, clear explanation, and workable proposals that support our vision of a world in which nanotechnology is widely used for productive and beneficial purposes, and where malicious uses are limited by effective administration of the technology.
Foreword on disobedience
“I am not a number! I am a free man!”
— Number 6, The Prisoner
“Afterward, I knew the rules, I understood what I was supposed to do, but I didn’t. I couldn’t. I was compelled to stay, compelled to disobey.”
— Agent Smith, The Matrix: Reloaded
Thomas Anderson was a disobedient fellow. He was frequently late for work. He didn’t do as he was told. He had a problem with authority. Fans of the first Matrix film identified with Thomas Anderson because of that rebelliousness. We all grinned when Thomas Anderson offered to give Agent Smith “the finger” in the interrogation room. So let’s imagine for a moment that our boy Tom had done what was expected of him. Suppose after being scolded by his manager, Tom learned his lesson, went back to his cubicle, and conformed.
Not much of a story. There’s Tom, working as he should in his cubicle. The end. Tom just became part of the machine. A robot. A machine.
As luck would have it, Mr. Anderson is compelled to disobey and we have a story after all. But it is not just about having a story. Not hardly. It is really about choice, which is what Neo realizes in the Architect’s chamber. When you get down to it, there are only two fundamental choices: you can choose to be robot or you can choose to be human; asleep or awake; dead or alive. Someone will always be telling you what to do. The robot, tin-chested and lifeless, does what he is told. The robot obeys. The human being disobeys. The human being gives Agent Smith the finger. The human being eats the apple.
The Architect gave Neo the same two choices. Neo chose not to be part of the machinery of the Matrix any longer. After that he was free.
P.S. If I could put 14 colors of flashing bold italics on the word “disobey” I would do that. Disobey. You are not a human being until you give the Man the finger.
Are Game Designers Auteurs?
When I created The Journal of Boardgame Design, one of my goals was to pull the nature of board game writing up a notch, beyond game reviews that were intended to be buyer’s recommendations and into the level of critical analysis. Treat games as an artform that could be analyzed in the same ways that music, painting, literature and film are treated. If this seems to raise game design to a level that isn’t warranted, we should remember that there were times when dance and film were regarded as merely recreation and entertainment. As game design has become more ambitious, so should its criticism.