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Bioinformatics

Bioinformatics Timeline here
Timeline of Bioinformatics
"Bioinformatics: History and Introduction",
by Luce Skrabanek, ICB, WMC, Cornell University, January 28, 2010.
"Methods for Incorporating Biological Information into the Statistical Analysis of Gene Expression Microarray Data",
by Debbie Leader, The University of Auckland, New Zealand, December, 2009.

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knowledge is power in bioinformatics
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Bioinformatics As Defined by HAL
Bioinformaticist vs Bioinformatician
Confusion over the definition of Bioinformatics
Other Definitions of Bioinformatics
Bioinformatics Articles by HAL
Bioinformatics Conference Reports by HAL
Bioinformatics Books by HAL
Quotables by HAL
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Theses on Bioinformatics
Articles on Bioinformatics
Lecture Slides on Bioinformatics
Lecture Notes on Bioinformatics
HAL's Curriculum Vitae
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Bioinformatics As Defined by HAL

(1987)

Bioinformatics is a new subject of genetic data collection, analysis and dissemination to the research community.

 

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(1994)

Since the coining of the word "bioinformatics" (See also Bioinformation and Rise of Bioinformatics ; Turbocharging Bioinformation) and the convening of the first international conference on the subject by HAL in the late 1980s, bioinformatics has undergone several stages of rebirths. In certain respects, the definition overlaps with that of computational biology and bioinformation infrastructure. In general, bioinformatics, computational biology, and ancillary computer supports (e.g., networking, hypertext, etc) taken together cover the whole spectrum of use of computers in biology-related sciences. There is really no sharp division between the two. However, there are two common distinctive features of bioinformatics and computational biology:

  1. techniques from other disciplines, especially computer science, are constantly being imported to help solve problems; and
  2. computers are a major tool in solving the problems.

Even though the three terms: bioinformatics, computational biology and bioinformation infrastructure are often times used interchangeably, broadly, the three may be defined as follows:

  1. bioinformatics refers to database-like activities, involving persistent sets of data that are maintained in a consistent state over essentially indefinite periods of time;
  2. computational biology encompasses the use of algorithmic tools to facilitate biological analyses; while
  3. bioinformation infrastructure comprises the entire collective of information management systems, analysis tools and communication networks supporting biology.

Thus, the latter may be viewed as a computational scaffold of the former two.

Since its humble beginning, the definition for bioinformatics has metamorphosized from the original and in many ways, naive, definition of data collection, analysis and dissemination to a current more encompassing definition. Its domain of application has also widened from being a special niche tool to that of an essential corporate technology. The scope has widened from a laboratory-based tool to an integrated corporate infrastructure.

Bioinformatics is currently defined as the study of information content and information flow in biological systems and processes. It has evolved to serve as the bridge between observations (data) in diverse biologically-related disciplines and the derivations of understanding (information) about how the systems or processes function, and subsequently the application (knowledge). A more pragmatic definition in the case of diseases is the understanding of dysfunction (diagnostics) and the subsequent applications of the knowledge for therapeutics and prognosis.

 

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A Bioinformaticist versus a Bioinformatician (1999)

Bioinformatics has become a mainstay of genomics, proteomics, and all other *.omics (such as phenomics) that many information technology companies have entered the business or are considering entering the business (see Computer Giants invest in Bioinformatics world), creating an IT (information technology) and BT (biotechnology) convergence. Because of this unprecedented phenomenon, HAL is regularly approached by consultants who are evaluating the market for companies considering entering the bioinformatics sector.

In almost all discussions and interviews, it became extremely clear that a distinction has to be made between a bioinformaticist and a bioinformatician.
A bioinformaticist is an expert who not only knows how to use bioinformatics tools, but also knows how to write interfaces for effective use of the tools.
A bioinformatician, on the other hand, is a trained individual who only knows to use bioinformatics tools without a deeper understanding.
Thus, a bioinformaticist is to *.omics as a mechanical engineer is to an automobile. A bioinformatician is to *.omics as a technician is to an automobile.

It has been argued that the professional categorization of bioinformatician and bioinformaticist may lead to some confusion. It is undeniable this may be the case. For example, a mathematician is an expert. However, we note that a physicist is an expert, so is a physician, except that they are in very different professions.

 

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Confusion over the Definition of "Bioinformatics" (2001)

An issue that regularly pops up is the definition of bioinformatics, particularly from individuals who are trying to get into the field. Most lament that there are too many definitions of bioinformatics.

This should be taken as an indication of the ubiquity of the subject. Bioinformatics, as both an enabling and enabled technology, will be defined differently depending on the domain of the person who is giving the definition. A computer scientist will give one definition, a biologist another, a biotechnologist yet another, and an individual from a pharmaceutical company will provide yet another definition.

Each definition is as good as the other. This is just the nature of the beast.

An important point to note is that bioinformatics is an enabling and an enabled tool, as such it will never replace the bench work and wet lab experiments of the biological, biochemical, health and clinical sciences. It only helps the areas it is being applied

  1. in eliminating unlikely candidates (such as in drug target discovery);
  2. in interrelating data and information (such as in analysis);
  3. in extrapolating into regime inaccessible by experiments (such as in cases not possible with current state of art of the technology);
  4. in studying cases that will be unethical to do (such as those studies that will be too invasive to the human body);
  5. etc...

Thus it would be unwise, particularly for bioinformaticists, to just write the best computer programs, or to just integrate the most sophisticated integrated packages to churn out numbers and beautiful graphics. The bottom line is still the biology, the biochemsitry, the healthcare system. Nothing, not the best software, nor the most sophisticated package, can replace real life systems.

 

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Other Definitions of "Bioinformatics"

  1. (Local Copy)   Definition of Bioinformatics as in Biomedical Informatics, Columbia University, New York.
  2. Bioinformatics as defined in Whitepaper Associates - A Technology Writers' Cooperative.
  3. Bioinformatics as defined by Therma Electron Corporation.
  4. Bioinformatics as defined by National Institutes of Health, USA, July 17, 2000.
  5. Bioinformatics as defined by Technology Grant News, page 9 of 16.

 

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Bioinformatics Articles by HAL

  1. "Bioinformatics in Communicable Diseases - The way forward", Asia Pacific Biotech, 14(12), December 2010, pp. 12-21.
  2. Biology as a Business Venture and the Rise of Bioinformatics, 1996.
  3. Bioinformatics & Cheminformatics in the Drug Discovery Cycle, 1997.
  4. Preface to Molecular Bioinformatics - Sequence Analysis, 1997.
  5. Viva bioinformatics, but who survives?, 1999.
  6. Informatics, Bioinformatics, and Binformatics, 2002.

  7. Other Bioinformatics articles by HAL.

  8. Translated (Chinese) Articles And Interviews, go to 生物信息學

 

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Bioinformatics Conference Reports by HAL and Colleagues

  1. Hwa A. Lim, and Richard Skoonberg, "Bioinformatics, Supercomputing, and Complex Genome Analysis", DOE/NIH Human Genome News, 4(5) January 1993.
  2. Hwa A. Lim, and Tauseef R. Butt "Bioinformatics takes charge", Trends in Biotech., Vol. 16 No. 3 (170), pp. 104-107, March 1998.
  3. T.V. Venkatesh, Benjamin Bowen, and Hwa. A. Lim, "Bioinformatics, pharma and farmers", Trends in Biotech., Vol. 17 No. 3 (182), pp. 85-88. March 1999.
  4. Hwa A. Lim, and T.V. Venkatesh "Bioinformatics in pre- and post-genomics eras", Trends in Biotech., Vol. 18 , pp. 133-135, April 2000.

 

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Bioinformatics Books by HAL

  1. Charles R. Cantor, and Hwa A. Lim (eds.), Electrophoresis, Supercomputing and the Human Genome, (World Scientific Pub. Co., New Jersey, 1991), 325 pages.
  2. Hwa A. Lim , James W. Fickett, Charles R. Cantor, and Robert J. Robbins (eds.), Bioinformatics, Supercomputing and Complex Genome Analysis, (World Scientific Pub. Co., New Jersey, 1993), 648 pages.
  3. Hwa A. Lim , and Charles R. Cantor, (eds.), Bioinformatics and Genome Research, (World Scientific Pub. Co., New Jersey, 1995), 529 pages.
  4. Ralf Hofest?t, and Hwa A. Lim (Hrsg.), Molecular Bioinformatics- Sequence Analysis, (Shaker Verlag, Aachen, Germany, 1997), 60 pages.
  5. Hwa A. Lim (Guest Editor), Pathways of Bioinformatics: from data to diseases, Special Issue of Briefings in Bioinformatics, Vol. 3(1), January, 2002 (Henry Stewart Publishers, London).
  6. Hwa A. Lim , GENETICALLY YOURS: Bioinforming, biopharming, and biofarming, (World Scientific Publishing Co., New Jersey, 2002), 417 pages.

 

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Theses on Bioinformatics

  1. "Methods for Incorporating Biological Information into the Statistical Analysis of Gene Expression Microarray Data", Debbie Leader, The University of Auckland, New Zealand, December, 2009.
  2. A Tool to Visualize ESTs, Delane Pereira de Oliveira Dias, San Carlos, December 2006. (In Portuguese)
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Articles on Bioinformatics

  1. Selected topics in bioinformatics, Hao Bai Lin, Fudan University, Shanghai, China, 2000.
  2. Computer giants invest in genomics, James Heckman, LocalBusiness.com, Dec 28, 2000.
  3. The market size of bioinformatics by Roger James, UK, in Drugs and Markets Bulletin, August 2001, UK.
  4. Biological data becomes computer literate by N. Goodman, USA, in Curr Opin Biotechnol. 2002 February; 13(1), pp. 68-71.
  5. Where chips and cells collide: Bioinformatics by Ayon Roy, India, in SiliconIndia, August 2002.
  6. Integration of bioinformatics resources: Critical need today, in Pharmabiz, Mumbai, July 31, 2003.
  7. Current challenges in Bioinformatics, by Joao Meidanis, in M.A. Nascimento, E.S. de Moura, and A.L. Oliveira (Eds): SPIRE 2003, pp. 16 - 27, (Springer-Verlag, Berlin, 2003).
  8. Informatica e biologia dei sistemi, by Corrado Priami, in Mondo Digitale, March, 2004. (In Italian language).
  9. Bioinformatics, virtual labs, and the human genome project, by Anne Cordon (University of Toronto) and Dr. Donna Messersmith (Howard Hugh Medical Institute), reprinted (pages 43-67) from Proceedingsof the 23rd Workshop/Conference of the Association for Biology Laboratory Education (ABLE), M.A. O'Donnell (ed), 2002, 392 pages.
  10. Bioinformatica ed intelligenza artificiale in Programmazione, December 25, 2004. (In Italian language).
  11. A brief history of genome research and bioinformatics in France by Antoine Danchin, Institut Pasteur, France.
  12. Bioinformatics and internet: New paradigm to dsiciplines and information technology, Shiva Kanaujia, SRELS Journal of Information Management, 41(1), March 2004, pp. 43-55.
  13. Modelling the dynamics of biosystems, Corrado Priami, and Paola Quaglia, Briefings in Bioinformatics, 5(3), September, 2004, pp. 259-269.
  14. Bioinformatics - N 2004, Leif Schauser, and Thomas Mailund, Bioinformatics Research Center, University of Aarhus.
  15. Information systems in the life sciences, Fons J. Verbeek, Imaging and Bioinformatics Group, Leiden Institute of Advanced Computer Science.
  16. Whats is bioinformatics?, Patrice Koehl's teaching pages.
  17. Bioinformatics: from data to diseases, Briefings in Bioinformatics, 2002, in DoCIS (Documents in Computing and Information Science).
  18. Form and Development of Bioinformatics, In: Journal of Henan Agricultural Sciences, November, 2002.
  19. The Bioinformatics System Architecture, Richard Casey, 2005.
  20. Monitoring Bioinformatics Web services requests and responses through a log-based architecture, Sergio Manuel Serra da Cruz, et al, In: XXV Congresso da Sociedade Brasileira de Computacao, 2005.
  21. Neural networks and machine learning in Bioinformatics - Theory and applications, Udo Seiffert, et al, In: ESANN'2006 Proceedings, Bruges, Belgium, April 2006.
  22. Evolution of dental informatics as a major research tool in oral pathology, Sasidhar Singaraju, H. Prasad, and Medhini Singaraju, Journal of Oral and Maxillofacial Pathology, 16(1), Jan-Apr, 2012, pp. 83-87.

 

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Lecture Slides on Bioinformatics

  1. Computational genomics by Prof. Benny Chor.
  2. Bioinformatics by Evelin Kozma.
  3. Bioinformatics by Dr. Craig Struble and Dr. Michael Thomas.
  4. Information systems in the life sciences by Dr. Fons J. Verbeek, Imaging & Bioinformatics Group, Leiden University, The Netherlands.
  5. Selected topics in bioinformatics, by Hao Bailin, Beijing Genomics Institute, Beijing, China.
  6. Multiple sequence alignment by Dr. Kung-Hao Liang, ITRI, Taiwan.
  7. Introduction to Bioinformatics by Dr. Tzi Tze Liang , Xiamen University, China.
  8. Bioinformatics: History and Introduction by Luce Skrabanek, Cornell University, New York, USA.
  9. Bioinformatics by Zhang Wen, Kumin Medical School, China.
  10. Bioinformatics: History, Present and Future , Peking University, China.
  11. Bioinformatics 1: Biology, sequences, phylogentics by Sepp Hochreiter, Johannes Kepler University Linz, Austria.
  12. China's National Grid - BioNode by Jun Wang, Beijing Genomics Institute, Beijing, Chna.
  13. Bioinformatics for the Practicing Pathologist by Gregory C. Critchfield, and Walter Knoll, College of American Pathologists.
  14. A Bioinformatics Study on Lymph Node Metastasis of Breast Cancers by Xuegong Zhang, Tsinghua University, Beijing, China.
  15. The Future of Bioinformatics by Dr. Hwa A. Lim, San Jose, California, USA.
  16. WinBioinfoTools: Bioinformatics Tools for Windows High Performance Computing Server 2008 by Mohamed Abouelhoda, Nile University, Cairo, Egypt.
  17. The Promise of Animal Genomics by Max Rothschild, Iowa State University, Iowa, USA.
  18. Introduction to Perl Programming for Bioinformatics, Alan M. Durham, University of San Paolo, Brazil, May 29, 2003.
  19. Computational Science: Building the future on science and computation, Teerakiat Kerdcharoen, Mahidol University, Thailand.
  20. An Introduction to Bioinformatics Algorithms: Molecular evolution, from www.bioalgorithms.info.
  21. IT Comes Alive, Azman Firdaus Shafii, Bioinformatics Symposium 2005, HELP University College, Malaysia.
  22. PCR and Primer Design, Dr. Mourad Aboul-Soud, King Saud University, January 2009.
  23. Bioinformatics: Introduction, Dr. Kahar Muzakhar, June 2011.

 

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Lecture Notes on Bioinformatics

  1. Computational Structural Bioinformatics, Prof. Patrice Koehl, University of California, Davis, (2007). (!!Highly recommended!!)

 

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Link to Other Valuable Bioinformatics Sites

  1. Wikiomics: Bioinformatics - defnition, active fields of research...
  2. Bioinformatics Directory - bioinformatics related news, books and web resources.
  3. The University of Albany, Science Library.
  4. (Local Copy)   The global technology revolution - bibliography on CIA Web site.
  5. Description of a software package SAGITTARIUS on Indiana University Web site.
  6. DNA and Protein Databases, Genomics..., Version 110, February 2009.

 

 

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Other Great Stuffs

  1. "Compuational Biology in Brazil", Goran Neshich, PLoS Computational Biology, 3(10), 2007.

 

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Something Different

  1. "Privacy, the Individual and Bioinformatics: A Buddhist Perspective", Soraj Hongladarom, Center for Ethics of Science and Technology, and Department of Philosophy, Chulalongkorn University, Thailand, 2007.
  2. "Bio-informatics - Taking a closer look from the scientific and business perspective", Nikko Hotel, Kuala Lumpur, Malaysia, September 23, 2002.

 

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Quotables by HAL

  1. "If you have $10 and I have $10, you give me your $10 and I give you my $10, we each still have $10. There seems to be a 'conservation of money'. If you have an idea and I have an idea, you give me your idea and I give you my idea. We each now have two ideas. Thus ideas propagate and the number of ideas multiplies."
    - Hwa A. Lim, Opening Remark, Bioinformatics and Genome Research, Inner Harbor Hotel, Baltimore, USA, 1996.
  2. Britton Chance (1913-2010) to Hwa Lim:
        "The nice thing about living to this age is that I out-survive all my [scientific] competitors, and few, if any, can contend with me the credits."
    Hwa Lim:
        "You are so humble. Your contributions to science are indisputable."
        " '8' is pronounced as 'pa' in Chinese, which is phonetically similar to the character 'fa' or prosperity. This will be a great year ahead for you. Many happy returns."
    [Britton of course lived for another 10 years till he was 97!]
    - Hwa A. Lim, sitting next to Britton Chance on the way to the Dallas/Forth Worth International Airport after delivering "Convergence of Biotechnology and Nanotechnology", October 18, 2001, Workshop in Honor of Britton Chance on his 88th Birthday, The University of Texas Southwestern Medical Center, Dallas, Texas, 2001.
  3. Exchanges on September 23, 2002, en route to lunch -
    Hal to James Cleeve:
       "You spoke about all the legal cases I am going to talk about tomorrow."
    Cleeve:
       "But I only touch on them. You will elaborate more on them."
    Frans:
       "Everything you want to say have been said. Only that no one listens."
    ...
       "My job today is to make sure you listen."
    - Hwa A. Lim, opening statement, "Patentability in Biotechnology", Bioinformatics Workshop - An odyssey of the Bioinformatics kind, J.W. Marriott Hotel, Kuala Lumpur, September 23-24, 2002, September 23, 2002.
  4. "People think that more information is always better. This cannot be further from the truth. Let me give you a counter example:
    When I was young, I had a date. On the way to send her home, we came upon a T-junction. Not knowing how to get to her home,
      I asked, 'Do I turn left or right?'
      She confidently responded, 'Left.'
    That was a useful piece of information - to get to her home, I had to turn left at the T-junction.
    Just as I was approaching the T-junction,
      She burst out, 'Maybe it is right?'
    Now she just nullified a 'good' piece of information.
    That was an eventful evening. We were at her home late - I had an extra hour with her, but much to her dad's chagrin, she was late for home. She was grounded for weeks.
    And mind you, those were the days before cellular phone existed. Grounded meant no communication, that is, no information."
    - Hwa A. Lim, Plenary Lecture, "Informatics, Bioinformatics, and Bininformatics", International Meeting on Frontiers of Physics, the Year of Physics to commemorate the centennial years of Einsteins 1905 breakthrough paper on relativity, The Mines, Kuala Lumpur, Malaysia, 2005.
  5. "We are trained to think of skills as something we develop for the workplace. But think of them as strengths, and they open up a huge number of opportunities. Learning to dance well is developing such a skill!"
    - Hwa A. Lim, chairing "Soar to New Heights" a fundraising event for Children with Special Needs, Milpitas, California, USA, February 26, 2011.
  6. "I have this bright idea; it is so bright that it burns out before I have the chance to tell anyone. What was your question again?"
    - Hwa A. Lim, on how dancing can help retard the onset of dementia, Silicon Valley, California, USA, 2011.

  7. "Sorry. I write many books; I do not write the same book many times [once published]."
    - Hwa A. Lim, when a publishing house editor asked if he would revise one of his best-selling books, San Jose, California, USA, December, 2011.
  8. "I did not choose bioinformatics, circumstances chose me.
    First of all, all things have to be situated - there have to be environments in which they can cause interactions and, so to speak, ask their own questions.
    I was using supercomputers at von Newmann Center at Princeton, I was at a supercomputer institute with all the computing resources, the genome project was just beginning, I had the good fortune to meet, among others, Charles Cantor, James Watson, Sydney Brenner... The timing was ripe, and I was at the right place.
    Whatever you want to claim, the truth is no genome project, no bioinformatics; no computing resources, no bioinformatics. That simple. That was about 1986, 1987."
    - Hwa A. Lim, at an interview about "bioinformatics", San Jose, California, USA, May, 2012.
  9. "I would prefer someone who brings along a seed to another who drags along a whole tree."
    - Hwa A. Lim, presiding over a meeting, Silicon Valley, California, USA, 2014.
  10. "Oh Jack Ma, I know him but he may not remember me."
    "We were both keynote speakers at conferences* in Silicon Valley in 2000. He spoke on e-commerce and I spoke on bioinformatics."
    "Now 15 years later, he is some $30 billion more famous than I am. He is phenomenal!"
    - Hwa A. Lim, when someone asked him about the record-making IPO of Alibaba, Silicon Valley, California, USA, September, 2014.
    * 'Silicon Valley Conference: Internet and Venture Investment' (August 25-26, 2000, Santa Clara Convention Center) and 'e-Venture: Now & Future' (August 27, 2000, Santa Clara Convention Center).
  11. "I am trained to be a scientist. I also have a social life, like other scientists, including some of those very famous ones, such as Albert Einstein who loved the violin, Richard Feynman who loved the bongos. But these famous people are so famous for their work that their hobbies are only mentioned in passing.
    In these days of social media, when I am out having fun with friends, they would video and post footages on social media, which soon get captured or archived on other social networks. So now I am better known as a fun-loving person than as a scientist.
    It took me more than 15 years of hard work to get a little recognition for my scientific work; now it takes less than a week to get noticed on the social media, for things good or silly. This is scary.
    Silly and funny things win the popularity contests on social media; science, not even close.
    Now you see how some candidates have been trying to tweet themselves into the White House in the 2016 presidential campaign? Substance, qualifications, experience do not matter as much.
    To answer your question, I am a scientist who loves to dance, and a very good one at it too!"
    - Hwa A. Lim, when a news anchor asked him if he was still a scientist, on World Dance Day, Silicon Valley, California, USA, April 29, 2016.
  12. "Everything that can have a chip in it will have a chip in it, and nearly everything with a chip in it will become a node in humanitys ever-growing big database"
    - Hwa A. Lim, in his keynote "From biodata to bigdata", at 2016 China Bio-medicine Industry Investment & Development Summit, in "Fortune 500 (Multinationals) into Jilin", South Lake Hotel, Changchun, Jilin, China, September 29, 2016.

 

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