Computational biology

Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. [1] The field is broadly defined and includes foundations in computer science , applied mathematics , animation , statistics , biochemistry , chemistry , biophysics , molecular biology , genetics , genomics , ecology , evolution , anatomy ,neuroscience , and visualization . [2]

Computational biology is different from biological computation , which is a subfield of computer science and computer engineering using bioengineering and biology to build computers , but is similar to bioinformatics , which is an interdisciplinary science using computers to store and process biological data.

Introduction

Computational Biology, which includes many aspects of bioinformatics , is the science of using biological data to develop algorithms or models to understand between various biological systems and relationships. Until recently, biologics did not have access to very large amounts of data which have become commonplace, particularly in molecular biology and genomics . Researchers were able to develop analytical methods for biological information, but were unable to share them quickly among colleagues. [3]

Bioinformatics began to develop in the early 1970s. It was considered the science of analyzing informatics processes of various biological systems. At this time, research in artificial intelligence was using the network of the human brain in order to generate new algorithms . This method of data acquisition is based on a large number of data sets. By 1982, information was being shared by the use of punch cards. The amount of data being shared began to grow exponentially by the end of the 1980s. This is the development of new computational methods in order to quickly analyze and interpret relevant information. [3]

Since the late 1990s, computational biology has become an important part of developing emerging technologies for the field of biology. [4] The terms computational biology and evolutionary computation have a similar name, but are not to be confused. Unlike computational biology, evolutionary computation is not concerned with modeling and biological data. It instead creates algorithms based on the ideas of evolution across species. Sometimes referred to as genetic algorithms, the research of this field can be applied to computational biology. While evolutionary computation is not inherently a part of computational biology, computational evolutionary biology is a subfield of it. [5]

Computational biology has been used to help the human genome, create accurate models of the human brain, and assist in modeling biological systems. [3]

Subfields

Computational anatomy

Main article: Computational anatomy

Computational anatomy is a discipline focusing on the study of anatomical shape and the visible or gross anatomical \ displaystyle 50-100 \ muscale of morphology . It involves the development and application of computational, mathematical and data-analytical methods for modeling and simulation of biological structures. The field is Broadly defined and includes foundations in anatomy , applied mathematics and pure mathematics , machine learning , computational mechanics , computational science , medical imaging , neuroscience , physics , probability , and statistics ; it aussi HAS strong connections with fluid mechanics andgeometric mechanics . It focuses on the anatomical structures being imaged, rather than the medical imaging devices. It is similar in spirit to the history of Computational Linguistics , has discipline That Focuses on the linguistic structures Rather than the sensor acting as the transmission and communication medium (s) .Due to the availability of dense 3D measurements via technology Such as magnetic resonance imaging (MRI), Computational anatomy has emerged as a subfield of medical imaging and bioengineeringfor extracting anatomical coordinate systems at the morphome scale in 3D.

In computational anatomy, the diffeomorphism group is used to study different coordinate systems by coordinate transformations as generated by the Lagrangian and Eulerian velocities of an anatomical configuration.3to another. Computational anatomy intersects the study of Riemannian manifolds where groups of diffeomorphisms are the central focus, intersecting with emerging high-dimensional theories of shape emerging from the field of shape statistics . The metric structures in computational anatomy are related to morphometrics , with the distinction that computational anatomy focuses on an infinite-dimensional space of coordinate systems transformed by diffeomorphism , hence the central use of terminology diffeomorphometrythe metric space study of coordinate systems via diffeomorphisms. At Computational anatomy’s heart is the comparison of shape by recognizing in one shape the other. This connects it to D’Arcy Wentworth Thompson ‘s Developments On Growth and Form qui HAS led to scientific Explanations of morphogenesis , the process by qui patterns are FORMED in Biology . The original formulation of Computational anatomy is a generative model of shape and form of exemplars acted upon via transformations. [6]

The spirit of this discipline shares strong overlap with areas Such As computer vision and kinematics of rigid bodies , Where objects are Studied by Analyzing the groups responsible for the movement in question. It is a branch of the image analysis and design theory at Brown University [7] pioneered by Ulf Grenander . Making spaces of an anatomical pattern in the shape of a metric space . The diffeomorphometry metric[8] of Computational anatomy measures how far two diffeomorphic changes of coordinates, which in turn turns to metric on the shapes and images indexed to them. The models of metric pattern theory, [9] [10] in particular group action on the orbit of shapes and forms is a central tool to the formal definitions in Computational anatomy.

Computational biomodeling

Main article: Modeling biological systems

Computational biomodeling is a field concerned with building computer models of biological systems. Computational biomodeling aims to develop and use visual simulations in order to assess the complexity of biological systems. This is accomplished through the use of specialized algorithms, and visualization software. These models allow for prediction of how to react to different environments. This is useful for determining if a system is robust. A robust biological system is one that “maintain their state and functions against external and internal disturbances”, [11]which is essential for a biological system to survive. Computational biomodeling generis a large archive of such data, allowing for analysis from multiple users. While current techniques focus on small biological systems, researchers are working on approaches that will be analyzed and modeled. A majority of researchers believe that this will be essential in developing modern medical approaches to creating new drugs and gene therapy. [11] A useful modeling approach is to use Petri nets via tools such as esyN [12]

Computational genomics (Computational genetics)

A partially sequenced genome.
Main article: Computational genomics

Computational genomics is a field within genomics which studies the genomes of cells and organisms. It is sometimes referred to as Computational and Statistical Genetics and encompasses much of Bioinformatics . The Human Genome Project is one example of computational genomics. This project looks to the entire human genome into a set of data. Once fully implemented, this could be used to analyze the genome of an individual patient. [13]This opens the possibility of personalized medicine, prescribing treatments based on an individual’s pre-existing genetic patterns. This project has created many similar programs. Researchers are looking at the genome of animals, plants, bacteria, and all other types of life. [14]

One of the main ways that genomes are compared is by homology . Homology is the study of biological structures and nucleotides in different organisms that come from a common ancestor. Research suggests that between 80 and 90% of genes in newly sequenced prokaryotic genomes can be identified this way. [14]

This field is still in development. An untouched project in the development of computational genomics is the analysis of intergenic regions. Studies show that roughly 97% of the human genome consists of these regions. [14] Researchers in computational genomics are working on understanding the functions of non-coding regions of the human genome through the development of computational and statistical methods and via large consortia projects such as ENCODE and The Roadmap Epigenomics Project .

Computational neuroscience

Main article: Computational neuroscience

Computational neuroscience is the study of brain function in terms of information processing structures that make up the nervous system. It is a subset of the field of neuroscience, and looks to analyze brain data to create practical applications. [15] It looks to model the brain in order to examine specific types of neurological system. Various types of models of the brain include:

  • Realistic Brain Models: These models look to represent every aspect of the brain. The most important information about the brain, but also the largest margin for error. More variables in a brain model These models do not account for parts of the cellular structure that scientists do not know about. Realistic brain models are the most computationally heavy and the most expensive to implement. [16]
  • Simplifying Brain Models: These models look at the scope of a model in order to assess a specific physical property of the neurological system. This allows for the intensive computational problems to be solved, and reduces the size of a realistic model. [16]

It is the work of computational neuroscientists to improve the algorithms and data structures currently used to increase the speed of such calculations.

Computational pharmacology

Computational pharmacology (from a computational biology perspective) is “the study of the effects of genomic data to find links between specific genotypes and diseases and then screening drug data “. [17] The pharmaceutical industryrequires a shift in analysis. Pharmacologists were able to use Microsoft Excel to compare chemical and genomic data related to the effectiveness of drugs. However, the industry has reached what is referred to as the Excel barricade. This arises from the limited number of accessible cells on a spreadsheet. This development leads to the need for computational pharmacology. Scientists and researchers develop computational methods to analyze these massive data sets. This allows for an efficient comparison between the data points and allows for more accurate drugs to be developed. [18]

Analysts project that if major medications fail to patents, that computational biology will be necessary to replace current drugs on the market. Doctoral students in computational biology are being encouraged to pursue care in post-doctoral positions. This is a direct result of major pharmaceutical companies needing more qualified analysts. [18]

Computational evolutionary biology

Computational biology has assisted the field of evolutionary biology in many capacities. This includes:

  • Using DNA data to reconstruct the tree of life with computational phylogenetics
  • Fitting genetics population models (Either forward time [19] or backward time ) to DNA data to make inferences about demographic or selective history
  • Building population genetics models of evolving systems.

Cancer computational biology

Cancer computational biology is a field that aims to determine future mutations in cancer through an algorithmic approach to analyzing data. Research in this field has led to the use of high-throughput measurement. High throughput measurement allows for the gathering of millions of data points using robotics and other sensing devices. This data is collected from DNA, RNA, and other biological structures. Areas of focus include determining the characteristics of tumors, analyzing molecules that are deterministic in causing cancer, and understanding how the human genome relates to the cause of tumors and cancer. [20]

Computational neuropsychiatry

Computational neuropsychiatry is the emerging field that uses mathematical and computer-assisted modeling of brain systems involved in mental disorders. It has been demonstrated by several initiatives that computational modeling is an important contribution to understand neuronal circuits that could generate mental functions and dysfunctions. [21] [22] [23]

Software and tools

Computational Biologists use a wide range of software. These range of programs are based on graphical and web-based programs.

Open source software

Open source software provides a platform for developing computational biological methods. Specifically, open source means that every person and / or entity can access and benefit from software developed in research. PLOSquotes four main reasons for the use of open source software including:

  • Reproducibility : This allows for researchers to use the exact methods used to calculate the relationship between biological data.
  • Faster Development: developers and researchers Instead they can use pre-existing programs to save time on the development and implementation of larger projects.
  • Increased quality: Having the input of many people in the field of insurance.
  • Long-term availability: Open source programs are not tied to any business or patents. This allows for them to be posted to multiple web pages and ensure that they are available in the future. [24]

Conferences

There are several broad conferences that are concerned with computational biology. Some notable examples are Intelligent Systems for Molecular Biology (ISMB), European Conference on Computational Biology (ECCB) and Research in Computational Molecular Biology (RECOMB).

Journals

There are numerous journals dedicated to computational biology. Some notable examples include Journal of Computational Biology and PLOS Computational Biology . The PLOS computational biology is a peer-reviewed journal that has many notable research projects in the field of computational biology. They provide reviews on software, tutorials for open source software, and display information on upcoming computational biology conferences. PLOS Computational Biology is an open access journal . The publication may be openly used provided the author is cited. [25] Recently opened a new journal Computational Molecular Biology was launched.

Related fields

Computational biology, bioinformatics and mathematical biology are all interdisciplinary approaches to life sciences that draw from quantitative disciplines such as mathematics and information science . The NIH describes computational / mathematical biology as the use of computational / mathematical approaches to address theoretical and experimental issues in biology and, by contrast, bioinformatics as the application of information science to understand complex life-science data. [1]

Specifically, the NIH defines

Computational biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. [1]

Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. [1]

While each field is distinct, there may be significant overlap at their interface. [1]

See also

  • International Society for Computational Biology
  • List of bioinformatics institutions
  • List of biological databases
  • Bioinformatics
  • Biostatistics
  • Computational chemistry
  • Computational science
  • Computational history
  • Computer simulation
  • Mathematical biology
  • Monte Carlo method
  • Molecular modeling
  • Network biology
  • Structural genomics
  • Synthetic biology
  • Systems biology

References

  1. ^ Jump up to:e “NIH working definition of bioinformatics and computational biology” (PDF) . Biomedical Information Science and Technology Initiative. 17 July 2000. Archived from the original (PDF) on 5 September 2012 . Retrieved 18 August 2012 .
  2. Jump up^ “About the CCMB” . Center for Computational Molecular Biology . Retrieved 18 August 2012 .
  3. ^ Jump up to:c Hogeweg, Paulien (7 March 2011). “The Roots of Bioinformatics in Theoretical Biology” . PLOS Computational Biology . 3. 7 : e1002021. doi : 10.1371 / journal.pcbi.1002021 . PMC  3068925  . PMID  21483479 .
  4. Jump up^ Bourne, Philip. “Rise and Demise of Bioinformatics, Promise and Progress” . PLoS Computational Biology . 8 : e1002487. doi : 10.1371 / journal.pcbi.1002487 . PMC  3343106  . PMID  22570600 .
  5. Jump up^ Foster, James (June 2001). “ionary Computation”. Nature Reviews .
  6. Jump up^ Grenander, Ulf; Miller, Michael I. (1998-12-01). “Computational Anatomy: An Emerging Discipline” . Q. Appl. Math . 56 (4): 617-694.
  7. Jump up^ “Brown University – Pattern Theory Group: Home” . www.dam.brown.edu . Retrieved 2015-12-27 .
  8. Jump up^ Miller, Michael I .; Younes, Laurent; Found, Alain (2014-03-01). “Diffeomorphometry and geodesic positioning systems for human anatomy” . Technology . 2 (1): 36-43. doi : 10.1142 / S2339547814500010 . PMC  4041578  . PMID  24904924 .
  9. Jump up^ Grenander, Ulf. General Pattern Theory: A Mathematical Study of Regular Structures . Oxford University Press. ISBN  9780198536710 .
  10. Jump up^ U. Grenander and MI Miller (2007-02-08). Pattern Theory: From Representation to Inference . Oxford: Oxford University Press. ISBN  9780199297061 .
  11. ^ Jump up to:b Kitano Hiroaki (14 November 2002). “Computational systems biology” . Nature . 420 (6912): 206-10. doi : 10.1038 / nature01254 . PMID  12432404 .
  12. Jump up^ Favrin, Bean (2 September 2014). “esyN: Network Building, Sharing and Publishing” . PLOS ONE . 9 : e106035. doi : 10.1371 / journal.pone.0106035 . PMC  4152123  . PMID  25181461 .
  13. Jump up^ “Genome Sequencing to the Rest of Us” . Scientific American.
  14. ^ Jump up to:c Koonin, Eugene (6 March 2001). “Computational Genomics” . Curr. Biol . 11 (5): 155-158. doi : 10.1016 / S0960-9822 (01) 00081-1 . PMID  11267880 .
  15. Jump up^ “BU Neuroscience” .
  16. ^ Jump up to:b Sejnowski, Terrence; Christof Koch; Patricia S. Churchland (9 September 1988). “Computational Neuroscience”. 4871. 241 .
  17. Jump up^ Price, Michael. “Computational Biologists: The Next Pharma Scientists?” .
  18. ^ Jump up to:b Jessen, Walter. “Pharma’s shifting strategy means more jobs for computational biologists” .
  19. Jump up^ Antonio Carvajal-Rodríguez (2012). “Simulation of Genes and Genomes Forward in Time” . Current Genomics . Bentham Science Publishers Ltd. 11 (1): 58-61. doi : 10.2174 / 138920210790218007 . PMC  2851118  . PMID  20808525 .
  20. Jump up^ Yakhini, Zohar. “Cancer Computational Biology” . BMC.
  21. Jump up^ Dauvermann, Maria R., Heather C. Whalley, André Schmidt, Graham L Lee, Liana Romaniuk, Neil Roberts, Eve C. Johnstone, Stephen M. Lawrie, and Thomas WJ Moorhead. “Computational neuropsychiatry-schizophrenia has a cognitive brain network disorder.” Frontiers in Psychiatry 5 (2014).
  22. Jump up^ Tretter, Felix, and Mr. Albus. “” Computational Neuropsychiatry “of Working Memory Disorders in Schizophrenia: The Network Connectivity in Prefrontal Cortex-Data and Models. Pharmacopsychiatry 40, no. S 1 (2007): S2-S16.
  23. Jump up^ Marin-Sanguino, A., and ER Mendoza. “Hybrid modeling in computational neuropsychiatry.” Pharmacopsychiatry 41, no. S 01 (2008): S85-S88.
  24. Jump up^ “The PLOS Computational Biology Software Section” . PLOS Computational Biology . 8 : e1002799. doi : 10.1371 / journal.pcbi.1002799 .
  25. Jump up^ “PLOS Computational Biology” .