The NIH Biomedical Computing Interest Group BCIG

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The NIH Biomedical Computing Interest Group
(BCIG)

• Mission
• To promote appropriate
• computing methodology
• in all aspects of
• biomedical research and patient care
• in support of
• the NIH mission.
• www.nih-bcig.org

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• In memory of
• Susan B. Harris
• a strong pillar of BCIG

We miss you dearly. Your BCIG friends
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(No Transcript)
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• A Tribute to Our Friend Susan Harris
• (delivered at Susans memorial service in the NIH
  Clinical Research Center Chapel on May 4, 2006)
• Susan and I both appeared at the very
  beginning of the NIH Clinical Center Department
  of Clinical Research Informatics (DCRI). We had
  office space near each other on Executive
  Boulevard, Democracy Boulevard, and in the
  Clinical Center. Because we shared close space
  and because we were very much alike in spirit,
  Susan and I became good friends. As typically
  happens in true friendships, we experienced some
  rough bumps along the way, but we both seemed to
  realize that our friendship was important and we
  were both determined not to let minor problems
  disrupt it. We worked through the difficult
  spots because we cared about each other and
  because we respected each other.
• Susan helped me tremendously with
  Scientific Computing and the NIH Biomedical
  Computing Interest Group (BCIG). On the day the
  she passed away, I told our ever-growing BCIG
  Community that she was a strong pillar of the
  BCIG and I really meant it. Susan supported BCIG
  in many ways she suggested topics, greeted
  speakers, and helped with advertising, room
  scheduling, listserver maintenance, and
  refreshments. She helped us deal with annoying
  red tape, awkward ill-defined policies, and
  difficult personalities. She was always
  available to take care of those last minute
  unexpected needs that arose, and she always took
  care of them patiently and with a smile. We are
  dedicating the entire BCIG May 2006 program to
  her, meaning that at all four events her picture
  will be shown and everyone will be reminded of
  her tremendous importance to BCIG.
• You know, Steve Rosenfeld and I often
  talked about the need for enhancing the culture
  in DCRI, something he and I were very enthused
  about but never seemed to find the time to
  address because of pressing deadlines and all
  that needed to be done to get CRIS up and
  running. Susan too was very interested in
  enhancing DCRI culture. I remember jokingly
  telling Susan that sometimes it seemed to me that
  the only culture we had around here is the yogurt
  in the refrigerator. She laughed and suggested
  that we have a DCRI yogurt lunch every month to
  talk about culture. Perhaps we could still do
  that in her honor. Are you interested?
• Susan had a great sense of humor and
  whenever I really needed a laugh, I would show
  her some of my silly cartoons or tell her some of
  my corny jokes. I could always rely on some
  sincere laughter from her even if she had seen
  the cartoon or heard the joke before. Susan was
  one of those rare people who knew that the joke
  didnt really matter. It was just an excuse to
  laugh, and to let down barriers.
• I sometimes see things in stores that
  will automatically remind me of someone. When
  this happens, I usually get the thing for the
  person. Shortly after Susan went into the
  hospital the first time, I came upon this Armored
  Wonder Woman action figure in the Big Planet
  Comics store in Bethesda. I immediately thought
  of Susan, and bought it for her. To me, Susan is
  a Wonder Woman. She was strong, wise and
  compassionate. She had a large sense of the
  importance of community life and she was always
  ready to offer sincere, meaningful help. I tried
  to get the action figure to her but for one
  reason or another it never quite made it to her.
  I hope Susans sisters, Christie and Polly will
  please receive it now as a token of my
  appreciation, respect, and love for Susan, who to
  me was and will always be a source of inspiration
  and strength - a true Wonder Woman.
• Jim DeLeo

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The NIH Biomedical Computing Interest Group
(BCIG)
Speakers on for audio
Please turn your speakers on.
Please turn your speakers on.

• We is a
• colorful
• lernanig ogrnaiztaion
• dedicated to joyous participatory learning
• while having fun !!!
• www.nih-bcig.org

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The BCIG Team

• Chairman . Jim
  DeLeo
• WEB Master . Ken Fang
  
• Meeting Master . Carl
  Leonard
• Brainstorming . Carl
  Leonard
• Tutorials . Jim
  DeLeo
• Speakers . Ken
  Fang
• BCIG Book Club . Jim DeLeo
• 
  Computers ... Carl Leonard
• 
  Biomedical ....... Jim DeLeo
• 
  People .... Kim Thompson
• Social Events . Carl
  Leonard Jim DeLeo
• Data Mining MRT . Carl Leonard
• BEST Chairman ............ Mo
  Al-Ubaydli

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BCIG Book Club Books for 2006 (www.nih-bcig.org)
PEOPLE
COMPUTER
COMPUTER
BIOMEDICAL
Apr 27
Mar 23
Feb 23
Jan 26
COMPUTER
BIOMEDICAL
PEOPLE
BIOMEDICAL
PEOPLE
When Mankind Forgot How to Think Emergence of
Machine Sapiens Prof. Kazem Sadegh-zadeh, MD.
May 25
Jun 22
Jul 27
Sep 28
Oct 26
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What can we do for each other?
What can we do for each other?
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Dialogue
Polite, friendly, sincere, meditative, group
inquiry
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BCIG May 2006 Program

• May 4 Brainstorming What Can We Do with
  an Artificial
• Neocortex at the NIH?
• Facilitators Carl Leonard,
  LIRED Corp. and
• Jim DeLeo, NIH-CC
• May 11 Tutorial Appropriate Use of
  Statistics for Big-Data
• Projects
• Instructor Laura Lee Johnson,
  Ph.D., NCCAM
• May 18 Speaker Event "Synthetic Gene
  Design Motivation,
• Challenges and Progress"
•                 Speaker Stephen J. Freeland,
  Ph.D. Univ. of Md.,
• Baltimore County
• May 25 Book Club Gen-e-sis The Scientific
  Quest for
• Lifes Origins On
  Intelligence, Robert Hazen
• Facilitator Robert Hazen,
  Ph.D. (author)

Information 301- 496- 0191
www.nih-bcig.org
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BCIG Brainstorming SessionThursday, May 4,
2006, 300 to 430 p.m. NIH Clinical Center
(Building 10) Medical Board Room (Room 2C116)
What Can We Do with an Artificial Neocortex at
the NIH?                                         
                 DESCRIPTION  This will be a
more focused continuation of the April 2006 BCIG
On Intelligence Book Club Meeting dialogue
which ended  with agreement to pursue the
following questions  (1) How can we build an
artificial neocortex? (2) What are some good
biomedical applications? (3) What questions can
we send to author Jeff Hawkins?  (4) How should
we format our meeting with Jeff when he comes to
the NIH in the Fall? If the idea of building a
mechanized (artificial) neocortex based on
present knowledge of how the real (human)
neocortex works for the purpose of addressing
hard biomedical problems appeals to you, please
look at the book, come to this BCIG Brainstorming
Session, and help us pick up the dialogue. (You
are welcome even if you dont look at the book.)
               FACILITATORS Carl Leonard and
Jim DeLeo will facilitate this brainstorming
session. Jim Is a computer scientist in the NIH
Clinical Center. He is the chairman of BCIG and
Chief of the Scientific Computing Section in the
NIH Clinical Center. Carl is an electrical and
computer engineer on contract to the NIH Clinical
Center Scientific Computing Section where he
works on data warehousing, data mining, data
visualization and podcasting projects with Jim.
Both Jim and Carl have experience building
artificial neural network systems for biomedical
applications.
Carl Leonard, LIRED Corp. Jim DeLeo, NIH-CC
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BCIG Speaker EventThursday, May 11, 2005, 300
to 430 p.m. NIH Clinical Center (Building 10)
Medical Board Room (Room 2C116)
Appropriate Use of Statistics for Big-Data
Projects DESCRIPTION Learn where big-data
projects such as fMRI, proteomics, and
microarray, can go astray from the statistical
and study design assumptions in ways that can
impede accurate interpretation of their resulting
data. How can you ensure the numerical
processing of your data does not hurt the
interpretability of its final outcome? Analysis
tools cannot compensate for any and all study
irregularities. Big-data usually costs
big-money. Make sure the data you get not only
fills drive space but also can be analyzed to
give you real answers to your real questions!
SPEAKER Laura Lee Johnson graduated with a BA
in mathematics from the University of Virginia
and a Ph.D. in biostatistics from the University
of Washington's School of Public Health and
Community Medicine. She was a pre-doctoral
trainee at the Northwest Veterans Affairs Health
Services Research and Development Center of
Excellence in Seattle and a Presidential Fellow
in the Department of Biostatistics at the
University of Washington where she taught
biostatistics to clinical fellows. She has
helped lead the biostatistics core in the Cancer
Prevention Studies Branch in the Center for
Cancer Research at the National Cancer Institute.
She now works as a statistician for the NIH
National Center for Complementary and Alternative
Medicine. Her research interests include analysis
of biomarker data, statistical methodology for
non-parametric joint modeling of longitudinal
and survival data, and longitudinal crossover
designs.
Laura Lee Johnson, Ph.D. NCCAM
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BCIG Speaker EventThursday, May 18, 2005, 300
to 430 p.m. NIH Clinical Center (Building 10)
Medical Board Room (Room 2C116)
"Synthetic Gene Design Motivation, Challenges
and Progress" DESCRIPTION An increasingly
common challenge of molecular biology is to move
genes from their 'natural' genomic context into a
'foreign' (heterologous) context for subsequent
manipulation and/or expression of their protein
product. It was largely assumed that challenges
here were purely technical once gene
manipulation was easy and cheap, the existence of
a standard genetic code should ensure
straightforward success for heterologous
expression experiments. The reality is now
recognized as a highly heterogeneous mixture of
success and failures. One of the key elements
emerging as a possible confounding factor
concerns codon bias the "spelling preferences"
that different genomes exhibit in their unequal
usage of synonymous codons. Here I will discuss
some of the work of my graduates in exploring
this phenomenon, from the analysis of "rules for
success" to the construction of a dedicated
database of "synthetic genes". SPEAKER  Drawing
on his background in evolutionary theory,
statistical analysis and computer programming,
Dr. Stephen J. Freeland studies the evolution of
the genetic code and its impact on genomic
evaluation with an increasing emphasis on
bioinformatics to genetic data analysis. He is
presently an assistant Professor in the
Department of Biological Sciences at the
University of Maryland Baltimore County (UMBC).
There, he also leads a research lab of Ph.D.,
Masters and undergraduate students in developing
an interactive web of bioinformatics tools for
genome exploration and analysis. He holds a
Ph.D. degree from the Department of Genetics,
Cambridge University, an M.Sc. degree from the
Departments of Biology and Computer Science,
University of York, and a BA degree from the
Department of Zoology, Oxford University, and he
has done extensive post-graduate work related to
his present position and interests at Princeton
University.
Stephen J. Freeland, Ph.D. University of
Maryland Baltimore County
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BCIG Book Club MeetingThursday, May 25, 2005,
300 to 430 p.m. NIH Clinical Center (Building
10) Medical Board Room (Room 2C116)
Gen-e-sis The Scientific Quest for Lifes
Origins DESCRIPTION Author Robert Hazen
doesnt tell us the meaning of life, but he does
shed light on how it started. The "primordial
soup" theory suggests that organic building
blocks floating around in Earth's ocean four
billion years ago combined to form the first
primitive organisms. Hazen explains many rival
theories vying for attention. The discovery of
life near hydrothermal vents deep in the ocean
have led some scientists to propose that life
started there. Recent studies of microbes living
in rock miles below the earth's surface suggest
more radical genesis stories. The origin of life
is a hotly contested scientific field, of which
Hazen provides a balanced view, airing all the
controversies. He discusses the study of
molecular fossils and even how we might search
for life on other planets. His writing is clear
and entertaining, giving a delightful look into
his unpredictable experimental work without
shying away from the complexity of the science.
(He coauthored Science Matters Achieving
Scientific Literacy.) AUTHOR Robert M. Hazen,
research scientist at the Carnegie Institution of
Washingtons Geophysical Laboratory and Clarence
Robinson Professor of Earth Science at George
Mason University, received the B.S. and S.M. in
geology at the Massachusetts Institute of
Technology (1971), and the Ph.D. at Harvard
University in earth science (1975). After
studies as NATO Postdoctoral Fellow at Cambridge
University in England, he joined the Carnegie
Institutions research effort.
Robert Hazen, Ph.D. George Mason University