Actions for Policy Makers and Employers

Given the broad remit of bioinformatics it is imperative for employers to recruit for their particular needs and assess how best to integrate bioinformaticians into the workplace. They need to ask themselves: 

• What is the task at hand? Although generally bioinformaticians are proficient at computational assignments, their role can become confused with other distinct yet complementary fields. For example building a software tool with a user interface as part of a new diagnostic test (software engineer) or creating a website for accessing a repository of pathology test results (website developer) do not necessarily require a grounding in ‘bio sciences’, and may be better suited to specifically trained individuals than bioinformaticians. 

• What ‘type’ of bioinformatician is needed? Bioinformatician is a catch all term and may not be a useful descriptor when recruiting for different roles within health services -  a ‘bioinformatician’ competent at creating databases and data archiving won’t necessarily have the skills to analyse and interpret the data sets they create. 

• How many bioinformaticians? It might be tempting to view bioinformaticians as a ‘Swiss army knife’ profession where one ‘tool’ can perform a multiplicity of jobs. In reality, introduction of innovative analytical technologies, such as genomics and Proterozoic into healthcare are likely to require multiple bioinformaticians with different skill-sets at different stages of implementation and service delivery. 

• What equipment will be needed? As with other scientific disciplines bioinformaticians require dedicated tools to perform their role. Access to suitable computational hardware, data storage capacity and servers, are just some of the fundamental structures. 

• How can we enable collaboration? Fostering interaction between bioinformaticians in different organisations, both within the health service and in academia, will enable adoption of best practices and collaboration to deliver innovation. Promoting this may be particularly important where bioinformaticians are recruited in isolation. 

• How can we support continued professional development (CPD)? Given the ever evolving nature of bio sciences data, an environment conducive to CPD is key to attracting and retaining talent, as well as sustaining innovation. 

Recruiting and Training Bioinformaticians for Health

 At present  individuals tend to enter the field from a range of undergraduate backgrounds (most commonly, biosciences, mathematics or computer science)  by either learning appropriate skills and knowledge ‘on the job’ or undertaking postgraduate training.  The multidisciplinary nature of bioinformatics requires practitioners to be flexible  to learning new skills and acquiring new knowledge (e.g. programming languages or biology) as the scope of the data and analyses with which they are working evolve.

It is less common for bioinformaticians joining the healthcare sphere to have experience of clinical genetics and operation of the healthcare system. The recent  NHS scientific training programme (STP) in bioinformatics and clinical bioinformatics is designed to be a training route for bioinformaticians within clinical specialties.

The objectives of bioinformatics

Bioinformatics is a broad discipline and often considered complementary, (if not equivalent) to the fields of computational biology and bio statistics. The overarching objectives of bioinformatics can broadly be categorized into the three key areas:

• analytical method development 

• construction and cu ration of computational tools and databases 

• data mining, interpretation and analysis

1. Analytical method development The construction and refinement of mathematical algorithms and statistical methods for the management and analysis of biological and bio medical data. Bioinformaticians function in a ‘research and development’ role, frequently applying statistical programming languages, mathematical modelling and computer simulations to design and implement methods for analyzing data. e.g. the development of algorithms to detect mutations in our genomes.

2. Construction and cu ration of computational tools and databases The collation, organisation and annotation of biological and medical data to aid its retrieval and analysis. Additionally the development and refinement of software tools that implement algorithms for analyzing biological and bio medical data. Bioinformaticians work in an ‘engineering’ capacity, typically using programming experience to develop bioinformatics workflows, databases and tools. e.g. the creation and maintenance of database resources cataloging information on genes and proteins.

3. Data mining, interpretation and analysis The extraction and analysis of data from databases or data sets using computational tools to derive biological or medical knowledge and insight from them. Bioinformaticians apply the above computational tools and analytical methods, as well use computer programming languages to extrapolate biological ‘meaning’ from data. e.g. the application of bioinformatics tools to predict protein structure and function. For a bioinformatician to deliver all these objectives would require a wide array of skills and deep understanding of many disparate domains of science. Like most scientists, individual bioinformaticians rarely possess the proficiency to fulfill all the possible objectives of their field. Instead they specialise according to their specific expertise and education, and work with other bioinformaticians, scientists and health professionals to achieve the broader objectives of their work.

The Roots of Bioinformatics for Healthcare

The term ‘bioinformatician’ is often used flexibly to describe someone working in a broad range of clinical or research ‘informatics’ domains. Originally describing the study of informatics processes in biotic systems1, bioinformatics today is a broad, interdisciplinary field that integrates principles from computer science, mathematics and statistics in order to manage, mine, visualize and analyse biological data. Bioinformatics has effectively co-evolved with disciplines such as genomics, and is now viewed as an integral component of these fields in academia. 

The number of healthcare organisations facing big data challenges, for example analysing genome sequence data, is also increasing rapidly. The consequent escalation in demand for the skills of bioinformaticians has not, however, always been matched by an increase in understanding of the capabilities and limitations of bioinformatics, or by preparedness for integration of this new class of healthcare scientists into the workforce. 

What then are the varied roles of bioinformaticians and what do UK health services need to do to maximise their skills for better, more effective patient care?

Defining the Role of Bioinformatician

Bioinformaticians are an increasingly important element of the healthcare workforce. As demand for their expertise grows, healthcare commissioners and providers need to consider how best to recruit, train, integrate, and manage Bioinformaticians to ensure UK health services can realize the benefits of the ‘big data’ revolution.

Bioinformatics 

An interdisciplinary field which combines concepts and knowledge from computer science, statistics and bio sciences in order to manage, mine, visualize and analyse biological and medical data. 

Clinical bioinformatics  

The clinical application of bioinformatics associated sciences and tools to inform the medical management of human disease.

Transnational Bioinformatics 

The development and application of bioinformatics techniques to optimize the transformation of data (basic molecular, genetic, cellular, and clinical) into clinical products or health implications.3,4

Health (medical) bioinformatics Specifically, the application of bioinformatics knowledge and tools to enable the collection and management of data for the delivery of health services.

A professional body?

As bioinformatic input has increasing impact on health service delivery, now is the time for a review of the standards of competence, ethics, conduct, and training needed for bioinformaticians in the health services. Currently there is no recognized professional group for bioinformaticians, nor a requirement for their professional registration. Consideration should be given to the desirability of professional registration and the establishment of a specialist group to determine standards of competency, ethics, conduct and training to ensure quality of services.

Bioinformatics MCQs Part 7

  

1.   When you are comparing two sequences of same or different organisms, what is the type of the alignment?
A. Global.
B. Local.
C. Pairwise sequence.
D. Multiple sequence.

2.    When you are comparing two or more than two sequences of same or different organisms, what is the type of the alignment?
A. Global.
B. Pairwise sequence.
C. Local.
D. Multiple sequence.

3.   Which alignment is useful to detect the highly similar sequences?
A. Pairwise sequence.
B. Local.
C. Global.
D. Multiple sequence.

4.   Which alignment is useful to detect the highly conserved regions?
A. Local.
B. Global.
C. Pairwise sequence.
D. Multiple sequence.

5.   The optimal alignment of two similar sequences is usually that _____ number of matches and ______ the number of gaps.
A. minimize, maximize.
B. maximize, minimize.
C. degrade, upgrade.
D. upgrade, degrade.

6.   Multiple sequence alignment method is called as ________alignment method.
A. global.
B. local.
C. progressive.
D. non-progressive.

7.  Which branching diagram is assumed to be an estimate of a phylogeny when branching lengths are proportional to the amount of inferred evolutionary change?
A. Phylogram.
B. Cladogram.
C. A guide tree.
D. Cardiogram.

8.   Profile Hidden Markov Models (HMMs) are important because they provide a powerful way to search databases for _______ related homologs. A. closely.
B. distantly.
C. new.
D. extra.

9.   Pfam-A and Pfam-B is automatically generated from the ______ database.
A. SMART.
B. PRINTS.
C. PROSITE.
D. PRODOM.

10.  Which database of Pfam is having high quality data?
A. Pfam-A.
B. Pfam-B.
C. Pfam-C.
D. Pfam-D.

____________________________________________

 Ans. 1- C, 2-D, 3-C, 4- A, 5-B, 6-C, 7-A, 8-B, 9-D, 10-A

Bioinformatics MCQs Part 2

• O coined the term Bioinformatics and when?
  A. Paulien Hogeweg, 1979.
  B. Dr. Margaret Oakley Dayhoff, 1976.
  C. Robert Ledley, 1978.
  D. David W Mount, 1977.

 

• Which one of the following is not a primary nucleic acid database?
  A. Gene Bank
  B. DDBJ
  C. EMBL
  D. TREMBL

 

• Which one of the following is a primary protein database?
  A. SWISS-PROT
  B. EMBL
  C. DDBJ
  D. NCBI

 

• _______ is a secondary database.
  A. DDBJ
  B. PROSITE
  C. NRDB
  D.OWL

 

• ______is a composite database.
  A. PROSITE
  B. DDBJ
  C. NRDB
  D. EMBL

 

• _______ is a primary protein structure database.
  A. PDB
  B. PubChem
  C. ChemBank
  D. SCOP

 

• Which one of the following is a secondary protein structure database?
  A. PubChem
  B. PDB
  C. ChemBank
  D. SCOP

 

• FASTA format starts with _______ symbol.
  A. /
  B. *
  C. >
  D. #

 

• Which one of the following is a complementary DNA database?
  A. Swiss-Prot
  B. GeneBank
  C. UniSTS
  D. NRDB

 

• HTGS is a division maintained by _______.
  A. NCBI
  B. PDB
  C. SCOP
  D. OWL

________________________________________
Ans. 1- A , 2-D, 3-A, 4- B, 5-C, 6-A, 7-D, 8-C, 9-C, 10-A

Bioinformatics MCQs Part 1

• The first bioinformatics database was created by
  A. Richard Durbin
  B. Dayhoff
  C. Michael j.Dunn
  D. Pearson

 

• SWISSPROT protein sequence database began in
  A. 1985
  B. 1986
  C. 1987
  D. 1988

 

• Analyzing or comparing entire genome of species
  A. Bioinformatics
  B. Genomics
  C. Proteomics
  D. Pharmacogenomics

 

• If you were using a proteomics approach to find the cause of a muscle disorder, which of the following techniques might you be using?
  A. creating a genomic library
  B. sequencing the gene responsible for the disorder
  C. developing physical maps from genomic clones
  D.determining which environmental factors influence the expression of your gene of interest annotating the gene sequence

 

• Shotgun cloning differs from the clone-by-clone method in which of the following ways? | Bioinformatics Questions
  A. The location of the clone being sequenced is known relative to other clones within the genomic library in shotgun cloning.
  B. Genetic markers are used to identify clones in shotgun cloning.
  C. Computer software assembles the clones in the clone-by-clone method.
  D. The entire genome is sequenced in the clone-by-clone method, but not in shotgun sequencing.
  E. No genetic or physical maps of the genome are needed to begin shotgun cloning.

 

• The tool for identification of motifs?
  A. COPIA
  B. Pattern Hunter
  C. PROSPECT
  D. BLAST

 

• Gene duplication has been found to be one of the major reasons for genome expansion in eukaryotes. In general, what would be the selective advantage of gene duplication?
  A. If one gene copy is nonfunctional, a backup is available.
  B. Larger genomes are more resistant to spontaneous mutations.
  C. Duplicated genes will make more of the protein product.
  D. Gene duplication will lead to new species evolution.

 

• You see that your lab partner is staring at a colorful Swiss-Prot page. He’s probably trying to
  A. translate a DNA segment into protein.
  B. find out structural and functional information about a protein he’s identified.
  C. determine how many harmful mutations have been reported in a certain gene.
  D. identify an amino acid sequence.

 

• A data base of current sequence map of the human genome is called
  A. OMIM
  B. HGMD
  C. GodenPath
  D. GenCards

 

• BLOSUM matrices are used for
  A. Multiple sequence alignment
  B. Pair wise sequence alignment
  C. Phylogenetic analysis
  D. All of the above

 

_________________________________________________
Ans. 1- B , 2-C, 3-B, 4- D, 5-E, 6-A, 7-A, 8-B, 9-C, 10-B

Why to study Bioinformatics?

• Bioinformaticians are in high demand in Academia, Research and Industry because few people have the education and skills to fill the available positions.
• Bioinformatics expertise is highly valued. Innovative and technological abilities and easy adaptation to changes are intrinsic traits of Bioinformaticians, broadening their employability in the modern scientific and technological societies undergoing permanent renewal.
• Learning bioinformatics is a determined bet to professional success. Bioinformaticians enjoy a vast range of research and professional jobs and earn competitive starting salaries.
• Bioinformatics is a transversal area, applicable to all sub-sectors of the life sciences. For Omics research, it is essential to handle and interpret large-scale data.
  

Challenges for Bioinformatics Field

 

1. Education: development of bioinformatics curricula.
2. Determining protein: DNA, protein: RNA, protein: protein recognition codes.
3. Mechanistic understanding of speciation.
4. Development of effective gene ontologies: systematic ways to describe gene and protein function.
5. Accurate ab initio protein structure prediction.
6. Precise models of where and when transcription will occur in a genome (initiation and termination).
7. Precise, predictive models of alternative RNA splicing.
8. Precise models of signal transduction pathways; ability to predict cellular responses to external stimuli.
9. Rational design of small molecule inhibitors of proteins.
10. Mechanistic understanding of protein evolution.

Bioinformatics Journals

 

Top 11 Bioinformatics Journals

1. Briefings in Bioinformatics
2. BMC Bioinformatics
3. DNA Research
4. Bioinformatics
5. In Silico Biology
6. Journal of Biomedical Informatics
7. Pattern Recognition
8. PLoS Computational Biology
9. Journal of Computational Biology
10. Artificial Intelligence in Medicine
11. Bio system

Nucleotide Sequence Databases

• INSDC
  The International Nucleotide Sequence Databases (INSD) have been developed and maintained collaboratively     between DDBJ , EMBL , and GenBank for over 18 years.
• ENA
  The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.
• RefSeq
  The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.
• GenBank
  GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
• DDBJ
  DNA Databank of Japan

Bioinformatics Events 2016

Conference:

CCEA--Ei 2016 : 2016 7th International Conference on Chemical Engineering and Applications (CCEA 2016)--Scopus, Ei
Location :Shanghai, China Date :Jul 7, 2016 - Jul 9, 2016 Conference Venue :Golden River-View Hotel Paper Publishing :CCEA 2016 papers will be published in Conference Proceedings, which is indexed by Ei Compendex, Inspec, and Scopus, or IJCEA (ISSN: 2010-0221).
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Call for Papers:

BIOEJ 2016 : Bioscience & Engineering: An International Journal
Submission Deadline: May 10, 2016
Notification Due : Jun 11, 2016
Final Version Due : Jun 22, 2016
Topics of Interest : Biochemical Engineering
Biochemistry
Bioinformatics
Health Informatics
Biomedicine
Bioscience Engineering
Biotechnology
Bio-fermentation Technology
Food Science & Technology
Genetics
Geomicrobiology
Molecular Biology of Plants
Zoophysiology

Paper Submission: Authors are invited to submit papers for this journal through E-mail bioejjournal@airccse.org.
Submissions must be original and should not have been published previously or be under consideration for publication while
being evaluated for this Journal.
Important Dates :
Submission Deadline : May 10, 2016
Authors Notification : June 11 , 2016
Final Manuscript Due : June 22 , 2016
Publication Date : Determined by the Editorial Board
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CEuro-Par Workshop:

4th International Workshop on Parallelism in Bioinformatics (proceedings published by Springer LNCS)
SUBMISSION DEADLINE: MAY 6, 2016
Dr. Miguel A. Vega-Rodriguez (mavega@unex.es)
http://arco.unex.es/mavega
ARCO Research Group
University of Extremadura
Dept. Technologies of Computers & Communications
Escuela Politecnica. Campus Universitario, s/n
10003 Caceres. SPAIN
Tel: +34-927-25-72-63
Fax: +34-927-25-71-87
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RGCB Workshop series:

HANDS-ON WORKSHOP ON THE DEVELOPMENT OF SIGNALING PATHWAY NETWORKS AND ANALYSIS OF TRANSCRIPTOMICS AND PROTEOMICS DATA
Dates :18 May 2016 - 20 May 2016
Location :Trivandrum, Kerala, India
Abstract: The current workshop will span theoretical understanding of the evolution of signaling networks from individual molecular
reactions and the integration of individual molecular reactions to build complex signaling networks. Further, this workshop also offer
the introduction to tools and methods involved in the identification of protein-protein interactions, enzyme-substrate reactions, post-translational
modifications, protein localization and expression of genes at the level of mRNAs, microRNAs and proteins. The practical sessions will introduce the
development and visualization tools and hands-on training in the development of signaling pathways. Importantly, the practical sessions would also
introduce the analysis of high-throughput data using open-access pathway analysis tools
Contact :Dr. Reshmi G;
Phone: [+ 91- 471-2781247];
Email: infoworkshop@rgcb.res.in Topics: Perspectives to Cell Signaling, Tools and Methods to study, Signaling Pathway Reactions,
Pathway curation strategies, Development of Signaling, Pathway Network Maps, Tools for Pathway Visualization,
Standard Community Formats, Pathway Resources, Pathway Analysis Tools,
Pathway Analysis of high throughput transcriptomics and proteomics data Related subject(s):Systems Biology and Computational Biology
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Bioinformaticians

Bioinformatics is the science of collecting and analyzing complex biological data such as genetic codes. Bioinformaticians apply information technology to Health research, Medical and Biological. They use computational tools to gather and analyze data in fields such as population, biology, genetics, and pharmaceutical development.