Sudhir Kumar talks with
ScienceWatch.com and answers a few questions about
this month's New Hot Paper in the field of Computer
Science.
Article Title: MEGA: A biologist-centric software
for evolutionary analysis of DNA and protein
sequences
Authors: Kumar,
S;Nei, M;Dudley, J;Tamura, K
Journal: BRIEF BIOINFORM
Volume: 9
Issue: 4
Page: 299-306
Year: JUL 2008
* Arizona State Univ, Biodesign Inst, Ctr Evolutionary
Funct Genom, A240, Tempe, AZ 85287 USA.
* Arizona State Univ, Biodesign Inst, Ctr Evolutionary
Funct Genom, Tempe, AZ 85287 USA.
(addresses have been truncated)
Why do you think your paper is highly
cited?
In this paper, we have discussed the motivation, design principles, and
priorities that have shaped the development of the Molecular Evolutionary
Genetics Analysis (MEGA) software. We credit these attributes to be the
primary reasons for the extremely high impact of the MEGA software package
across a broad range of biological disciplines.
In addition to the users of MEGA, other software developers have found our
design principles to be compelling, which indicate that the principles are
positively influencing the design and implementation of other
bioinformatics software packages.
Does it describe a new discovery, methodology, or
synthesis of knowledge?
This paper discusses a biologist-centric paradigm for developing software
for biologists. Biologist-centric software solutions are not only
user-friendly, but also emulate the common workflows and habits of
biologists.
"We are building on the successful
design patterns of MEGA for a software
package that responds to the requirements of
biologists in this era of personal genomics
and high-throughput
sequencing."
In addition, we present examples from the MEGA software which recognize
that the burden is on bioinformatics software developers to inform users
about the precise nature of the results generated and also to develop new
applications and adapt existing ones to multiple platforms.
Would you summarize the significance of your paper
in layman's terms?
This paper presents a synthesis of knowledge on biologist-centric software
designs that we've developed, which has come to be appreciated over the
course of the MEGA development for a period of almost two decades.
Therefore, software developers may find some of our principles to be useful
in developing effective bioinformatics software designs for biologists.
How did you become involved in this research, and
were there any problems along the way?
We initiated the MEGA software project due to our own need for employing
statistical methods in the comparative analysis of DNA and protein
sequences in the early 1990s. At this time, most computer programs
available did not allow us to explore the primary data visually and lacked
a user-friendly interface.
In order to make statistical methods available for phylogenetic analysis in
a user-friendly manner, we produced a user-friendly program with a
mouse/menu interface for use on early PCs in 1993. Over the last 15 years,
MEGA has undergone many transformations and an extensive expansion. The
most recent version of MEGA (version 5.0) is scheduled to be released later
this year.
Where do you see your research leading in the
future?
We are building on the successful design patterns of MEGA for a software
package that responds to the requirements of biologists in this era of
personal genomics and high-throughput sequencing. The need for
biologist-centric solutions has become even more acute because the
researchers, especially those without extensive informatics training, wish
and need to analyze large and diverse datasets in their daily
investigations.
Biological researchers would like to exploit the extensive genome
information more effectively and efficiently while avoiding the need to
navigate the complexity and size of the raw data available in public
databases.
Do you foresee any social or political implications
for your research?
Perhaps not in the grand scheme of life, but within academic circles it
carries social implications for the expectations that researchers and
granting agencies should, and most likely will have, when it comes to using
and funding bioinformatics software projects.
Sudhir Kumar, Ph.D.
Professor
Center for Evolutionary Functional Genomics
The Biodesign Institute
School of Life Sciences
Arizona State University
Tempe, AZ, USA Web |
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