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| DATE | 2018-02-04 |
| FROM | Ruben Safir
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| SUBJECT | Subject: [Learn] Biological Computation Sciences and Informatics
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From: Ruben Safir
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This is just an initial work of a potentially larger proposal:
February 2nd, 2018
Proposal for Bioinformatics and Biocomputational Mathmatics Program
Long Island University
Brooklyn, USA
Prepared by Ruben Safir
Comp Sci MS 2016
BS Pharmacy 1988
Initial Statement:
Long Island University, Brooklyn Campus is of a full service University
which has historically serviced underserviced populations within the
outer-boroughs of New York City. While it has a strong liberal arts
background, the school has increasingly become focused on the career
path for students within the healthcare sector, as this has provided job
ready skills for its student population and their families. But LIU is
in no way a business school. While it competes in that sector, the
school is a full service university with well funded and essential
programs in the arts, sports, dance, and advanced programs in research.
The school was also a pioneer in the information systems field, being
an early participant in gophernet and the early adopter of worldwide web.
Currently, the school has large programs in Pharmacy, Nursing,
Physicians Assistance, Sports Health, Healthcare Management, Speach
Pathology, and other areas in the allied health field. The pharmacy
school includes a well respected PhD program in pharmacuetics. This has
required the university to maintain a mathmatics department which is
under utilized. These programs position us well for one of the upcoming
explosive areas of economic activity within New York City, which is the
field of Biocomputational Mathmatics. Universities in New York are now
focusing on this area of computational biology. Hunter College, NYU,
Colombia University, and the hospital university complexes within the
city are focused on these areas. Much of it is a natural outgrowth of the
genometic work in the wake of the Human Genome project well over a
decade ago. More of it is being stimulated as high school students
entering universities with skills and backgrounds in gene splicing
technology. The government itself has targeted biological technology
for its enterprise centers. The New York Economic Development
Corporation has specifically targeted the life sciences for the same
reasons I outlined in this report. It will be an economic engineer for
the immediate future and into the next century.
The city already has the deepest resources in the nation in the area of
life science technologies. The development of these areas is critical
to the city's economic future.
(https://www.nycedc.com/industry/life-sciences). Our participation in
this feild will be essential to providing critical education for our
local student population. And the computer science department is
positioned within the university to weave together these different
departments into a productive research center in biotechnology. The
combination of the Enterprise Center, the Pharmacy research facilities,
our allied health science programs, and our MBA programs puts us in a
strong growth position for the future. By pulling shared resources from
the entire campus, we can place the department and the university on its
most solid financial foundation by providing real skills and promise of
future employment for a broad number of students at different levels.
Instead of competing with business schools for students who want to
enter and increasingly saturated nursing environment, we will lay out
vibrant, satisfying, expansive career paths for a representative
population which is often short on long term vision, and left behind in
a changing economy.
Project Goals:
The Computer Science department should create 2 Bachelors Degree minors,
and 3 Masters Degree Programs and collaborate for 1 Doctor program.
The programs will be interleaved, which should achieve certification for
all the programs with minimal additions to current programs. They can
be roughly outlined as follows:
BS minors: Computer Sciences: Biological Computations and Statistics
Computer Sciences: Biology Informatics and Informations Systems
Management.
=
Masters Degrees:
Computational Biology
Masters of Business Degree in Healthcare Program Management
Healthcare Information Systems
Doctoral Degree:
Biological Computations and Phylogenetics
Descriptions:
Computer Sciences: Biological Computations and Statistics - is a minor
offered by the Computer Science Department which has a focus on
biological statistics and computational algorithms. It would require
2 years of Biology, genetics, Linear Algebra, Calculus to the second
level, C,
C++. Java, Python, and R programming taught through Algorithms,
Artificial Intelligence, Unix Systems, a semester of Phylogeny, a
semester of microbiology, a semester of biological statistics with R
programming, and data analysis. It is a very intensive BS on par
with many healthcare programs.
=
Computer Sciences: Biology Informatics and Information Systems - is
a minor offered by the computer science department which has focus on
systems programming, and statistical analysis of healthcare data. It
would require Linear Algebra, Systems Programming and UML, biological
statistics, one semester on digital medical equipment and hospital
information systems. It's goal is to create users capable of
understanding and controlling the flow of healthcare data in the
institutional setting, including understanding of billing coding
systems, Seamans systems, pyxus and other medical dispensing devices,
and healthcare monitoring and imaging programs.
=
Masters Degree of Computational Biology:
Masters degree which can be entered by either the biological or
computer sciences. It would requirement for Computer Science Majors
of core programming, Algorithms, Networking, Database Principles,
Communications, Compiler Theory, Parallel Programming and
Computational Mathematics. For Biology and Life Sciences students,
they would need to have coursework microbiology, pharmacology,
biochemistry, genetics, and core mathematics to Calculus Two.
The program itself will concentrated on R programming being used to
teach phylogeny, biological statistics, Markov chain, Bayesian
statistics, Neural Networks, and molecular computations.
See: Biological Computation Ehud Lamm, Ron Unger, SBN 9781420087956 -
CAT# C7959
=
https://ocw.mit.edu/courses/biology/7-349-biological-computing-at-the-cross=
roads-of-engineering-and-science-spring-2005/
This is an MS degree designed for students interested in research and
is intense. There is placement opportunities for graduates
worldwide.
=
Masters of Business Degree in Healthcare Program Management:
This is an MBA specializing in the specific needs for information
management within the healthcare system. Hospitals and Healthcare
organizations are enormous consumers of information systems and the
management of such systems requires specialized knowledge in the
areas of biology, government regulation, and medical equipment. Many
of these systems are designed and created in corporate black boxes
and protected by international copyright and patent law. Trying to
decipher these competing interests and regulations needs a well
educated and experienced individual with a strong understanding of
systems programming and business management. It is also necessary to
understand epidemiology, and the funding and usage of research
facilities with the context of the healthcare system.
Masters Degree in Healthcare Information Systems:
This is a Computer Sciences major with an focus on healthcare
informatics. This would include advanced database programming,
biological statistics, big data and artificial intelligence with
emphasis on real time clinical data delivery and educational
facilities in support of clinical services. This would include
networking, fundamental cryptography, expert systems, and the
fundamentals of data types, such as the formats of CT images, and so
on. This would also include drug information systems, laboratory
data, and relevant clinical library access.
Doctoral Degrees Biological Computations and Phylogenetics:
This would be a research driven PhD program which focuses on specific
areas of biological research using computational sciences. It can
apply to a wide range of research problems and might depend on
collaboration with external departments and funding opportunities.
By emphasising on the computational math and programming, we make
ourselves available to a wide range of biological problems which in
practice and theory, overlap. Computational problems that involve
protein folding use the same computational theory as evolutionary
phenology, or even tools in ecological studies. The department can
share problems with the Pharmaceutics PhD in the Pharmacy school or
create new opportunities in the Masters Degree program in Biology,
Chemistry, and Nursing.
This program would need a solid background in programming languages,
compiler theory, computational mathematics and statistics, advanced
calculus, differential equations, parallel programming, and core
education in the R programming language, with advanced skills in the
C family, the Java family, and python. Artificial intelligence
libraries in Python and other languages need to be mastered and
understood. For several reasons, R programming has become central to
the biological sciences and it should be the focus of most research
at this time, although it should in no way be the exclusive tool.
The program should extend itself to post graduate studies, and funding
from a number of grant streams. NIH, Pharmaceutical companies, start
up businesses, and economic development grants can support this
research and allow it to grow. Opportunities exist to share research
with both local and overseas programs, even to cross pollinate and to
share scholars in joint ventures with Ariel University in Israel.
the core text, or "bible" accepted in this area of study is
"Biological Computation (Chapman & Hall/CRC Mathematical &
Computational Biology) by Ehud Lamm and Ron Unger" from Bar Ilan
University. There are also local research labs at Hunter CUNY, Columbia
University, NYU, and Cornell. NYCTC CUNY has a BS program in
downtown Brooklyn.
The University doesn't need to completely break new ground.
Currently there are programs many programs to use as templates:
=
*NYCTC CUNY,
(http://www.citytech.cuny.edu/biological/biomedical-informatics-bs.aspx)
PROGRAM-SPECIFIC DEGREE REQUIREMENTS 76-77 CREDITS
Biological Sciences and Molecular Informatics (37 credits)
BIO 1101 Biology I 4
BIO 1201 Biology II 4
BIO 2311 Human Anatomy and Physiology I 4
BIO 2312 Human Anatomy and Physiology II 4
BIO 3350 Bioinformatics I 4
BIO 3352 Bioinformatics II 4
BIO 3354 Computational Genomics 3
BIO 3356 Molecular Modeling in Biology 3
BIO 3526 Pathophysiology 3
BIO 3620 Molecular and Cell Biology 4
Computer and Healthcare Informatics (18 credits)
MED 2400 Medical Informatics Fundamentals 3
MED 4229 Healthcare Databases 3
CST 1101 Problem Solving with Computer Programming 3
CST 1201
CST 2403 Programming Fundamentals
OR
C++ Programming I =
3
CST 1204 Database Systems Fundamentals 3
HSA 3510 Health Services Management I 3
Internship/Research Course
MED 3910 Internship/Research in Biomedical Informatics
They also have:
Applied Mathematics-Science/BS
The applications of mathematics in this industry include designing
experiments to test drug safety and effectiveness, creating computer-based
models of the spread of disease and assessing the risks of different
medical treatments.
BIO 1101 Biology I 4
BIO 2311 Human Anatomy and Physiology I 4
CST 1101 Problem Solving with Computer programming 3
CST 2403 C++ Programming I 3
CST 3503 C++ Programming II 3
CHEM 1110 General Chemistry I 4
CHEM 1210 General Chemistry II 4
CHEM 2223 Organic Chemistry I 5
MAT 1475 Calculus I 3 4
MAT 1575 Calculus II 4
MAT 2440 Discrete Structures and Algorithms I 3
MAT 2572 Probability and Mathematical Statistics I 4
MAT 2580 Introduction to Linear Algebra 3
MAT 2630 Applied Mathematics Technology =C3=A2=E2=82=AC=E2=80=9C Numerical=
Methods 3
MAT 2675 Calculus III 4
MAT 2680 Differential Equations 3
MAT 3672 Probability and Mathematical Statistics II 4
MAT 3770 Mathematical Modeling I =C3=A2=E2=82=AC=E2=80=9C Optimization 3
MAT 3772 Stochastic Models 3
MAT 3880 An Introduction to Partial Differential Equations using
Mathematical Methods in Biology 3
MAT 4672 Computational Statistics 4
MAT 4900 Internship I 2
MAT 4901 Internship II 2
Electives (select as needed to add up to 784)
BIO 2312 Human Anatomy and Physiology I 4
CHEM 2323 Organic Chemistry I 5
MAT 2540 Discrete Structures and Algorithms II 3
MAT 3777 Applied Mathematics Applications of the Wave Equation 3
MAT 3787 Applied Mathematics =C3=A2=E2=82=AC=E2=80=9C Finite Fields 3
MAT 3788 Applications of the Heat Equation for Financial Mathematics 3
MAT 4788 Financial Risk Modeling 3
MAT 4872 Probability and Mathematical Statistics III 4
MAT 4880 Mathematical Modeling II
*Hunter CUNY has an advanced program that includes a research lab
(http://www.hunter.cuny.edu/qubi)
QuBi -at-Hunter College
Hunter's interdisciplinary program in Quantitative Biology/Bioinformatics
Hunter College is one of only nine institutions of higher education
in the country to offer an interdisciplinary program in quantitative
biology. Students majoring in Biology, Chemistry, Computer Science,
Mathematics or Statistics can add a quantitative biology concentration
to their major. Among the many benefits of this innovative program
are access to competitive scholarships, small classes, training by a
multidisciplinary team of research scientists and dedicated academics,
individual mentoring, the opportunity to participate in research conducted
at Hunter and nationally, topnotch preparation for graduate studies and
for scientific careers in this new frontier.
Qubi concentrators will learn statistical and computational methods
and how to apply those methods to the processing, storage, analysis,
visualization and modeling of large-scale molecular biological data.
They will develop the research, communication and collaborative skills
to contribute to the solution of problems in bioinformatics as members
of a multidisciplinary team.
(http://qiu.bioweb.hunter.cuny.edu/)
(http://diverge.hunter.cuny.edu/labwiki/Main_Page)
*CUNY Graduate Program:
(https://www.gc.cuny.edu/Page-Elements/Academics-Research-Centers-Initiativ=
es/Doctoral-Programs/Computer-Science/Research-Areas/Computational-Biology)
One particularly important program is in the Microbiology Department of
the University of Michigan run by Dr. Patrick Schloss. He collaborates
nation wide and is revolutionary in microbiology education by making
biological computation a core requirement for their Microbiology
program. His world famous research lab produced Muther in the R
programming language (https://www.mothur.org/). Mothur is described as:
This project seeks to develop a single piece of open-source,
expandable software to fill the bioinformatics needs of the microbial
ecology community. In February 2009 we released the first version
of mothur, which had accelerated versions of the popular DOTUR
and SONS programs. Since then we have added the functionality of a
number of other popular tools. mothur is currently the most cited
bioinformatics tool for analyzing 16S rRNA gene sequences. Step
inside the wiki and user forum and learn how you can use mothur
to process data generated by Sanger, PacBio, IonTorrent, 454, and
Illumina (MiSeq/HiSeq). If you would like to contribute code to
the project feel free to download the source code and make your
own improvements. Alternatively, if you have an idea or a need,
but lack the programming expertise, let us know and we'll add it to
the queue of features we would like to add. Our current goal is to
release a new iteration of the project every couple of months
This is exactly the kind of research that every department in our
healthcare program can be involved with.
As for careers: We are already positions for many career level
positions in the city. A quick search on Indeed.com for Computational
Biologist turns up the following results:
Research Position (Various Levels), Systems Biology
Simons Foundation - 3 reviews - New York, NY 10010 (Gramercy area)
Experience in mathematics or computational biology. PhD in computer
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30+ days ago - save job - more...
Data Scientist, Engineering
Google - 2,046 reviews - New York, NY 10011 (Chelsea area)
(e.g., as a statistician / data scientist / computational biologist /
bioinformatician). 4 years of relevant work experience (e.g., as a
statistician /...
8 days ago - save job - more...
Data Scientist, Modeling Team
Applecart - 2 reviews - New York, NY
(e.g., as a statistician / data scientist / computational biologist /
bioinformatician). Applecart deploys proprietary technology to run
smarter advertising...
Easily apply
1 day ago - save job - more...
Drug Discovery Scientist
Schrodinger - New York, NY
If you are a computational chemist or modeler and have an interest in
applying cutting-edge computational approaches to structure-enabled
projects, we are eager...
30+ days ago - save job - more...
Data Scientist - Everyday Health
Ziff Davis, LLC - 5 reviews - New York, NY 10016 (Gramercy area)
(e.g., as a statistician / data scientist / computational biologist /
bioinformatician). MS degree in a quantitative discipline (e.g.,
statistics, operations...
30+ days ago - save job - more...
Drug Hunter - Computational Chemist
Schrodinger - New York, NY
Extensive experience in medicinal and/or computational chemistry. Our
drug discovery group of over 40 scientists includes designers, modelers,
computational...
22 days ago - save job - more...
Drug Hunter - Medicinal Chemist
Schrodinger - New York, NY
Our drug discovery group of over 40 scientists includes designers,
modelers, computational chemists, medicinal chemists, crystallographers,
biochemists, and...
30+ days ago - save job - more...
Computational Biologist I
Memorial Sloan Kettering - 582 reviews - New York, NY
Work with experimental and computational biologists, clinical and
translational research collaborators, and scientists across MSKCC....
23 days ago - save job - more...
Research Technician I
Howard Hughes Medical Institute - 66 reviews - New York, NY
They will assist investigators in research activities and contribute to
research in developmental and molecular biology by performing a variety
of techniques,...
30+ days ago - save job - more...
Postdoctoral Associate
Weill Cornell Medicine - 46 reviews - New York, NY
The laboratory (a 2017 recipient of the NIH Directors Pioneer Award) is
a rapidly growing program/laboratory benefitting from exceptional
resources, scientific...
Easily apply
19 days ago - save job - more...
My recent searches
Biological Computional - Brooklyn, NY
Biological Compution - Brooklyn, NY
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Distance:
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Job Type
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Contract (2)
Location
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Company
Memorial Sloan Kettering (7)
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more =C2=BB
Experience Level
Mid Level (13)
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Assistant Vice President - Data Scientist
BNP Paribas - 1,689 reviews - New York, NY
At least 1 year of relevant work experience (e.g., as a statistician/
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Principal Scientist
Schrodinger - New York, NY
Extensive experience in medicinal and/or computational chemistry. Our
drug discovery group of over 40 scientists includes designers, modelers,
computational...
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Sr. Computational Biologist
Memorial Sloan Kettering - 582 reviews - New York, NY
Computational Biologist will work with an expanding team of research,
clinical and computational investigators working in cancer genomics....
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Drug Designer
Schrodinger - New York, NY
Computational chemistry experience. Our drug discovery group of over 40
scientists includes designers, modelers, computational chemists,
medicinal chemists,...
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Senior Scientist, Protein Structure Prediction / Homology Mo...
Schrodinger - New York, NY
Schr=C3=B6dinger has over 300 engineers, computational chemists, medicinal
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As a Computational Biologist / Bioinformatics Analyst you will:. Work
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The Biomarker Development Department works in partnership with Novartis
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We have removed 3 job postings very similar to those already shown. To
see these additional results, you may repeat your search with the
omitted job postings included.
Reviewing these results one might conclude that if our Pharmacy program
is to remain relevant that we might need to collaborative effort.
-- =
So many immigrant groups have swept through our town
that Brooklyn, like Atlantis, reaches mythological
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