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How to Become a Bioinformatician

If you want to start a journey towards being a bioinformatician, you must first know the meaning of the term bioinformatics. You will also need to know what bioinformaticians do, and what you need to know to land your first entry level job as a bioinformatician.

Most bioinformaticians work within different medical science and health fields, including biology, genetics, proteomics, and pharmaceuticals. Some professionals come from a biomedical research background while others specialize in computational tools.

The Bioinformatician

A bioinformatician not only uses tools for understanding or solving biological problems, but also participates in developing tools for research. Bioinformaticians comprise of two types.1 The first category includes developers who implement algorithms and develop tools for bioinformatics. The second category includes curators who are responsible for all the work related to data resources and data integration.

Skills Required to Be a Bioinformatician

Bioinformatics Skills – You need to learn how to use:2,3

  • Sequence alignment tools such as Blast or Bowtie
  • The Genome Analysis Toolkit (GATK)
  • Software for Next Generation Sequencing, Microarray, qPCR, and Data Analysis (Partek)
  • Tools for handling high throughput sequencing data like (samtools)
  • To get gene data sets use a tool such as (Ensemble)
  • Tools for database search systems like (Entrez)

Statistical Skills – You need to learn:

  • Statistical software systems such as SPSS and SAS
  • How to do statistical analyses with Python or R

Programming Skills – You should be familiar with:

  • One or more of these programming languages: R, Perl, Python, Java and Matlab
  • Machine learning tools and libraries such as Mllib and Scikit-Learn in python are very useful to learn

Biology Knowledge – This requirement will vary according to your domain of study or the particular job you are applying to. You will most likely need knowledge about molecular biology, genetics, cancer biology, and/or modern biology.

Genomic and Genetic Knowledge – This knowledge is the core of bioinformatics. Some of the most important skills are high-throughput sequencing, next generation sequencing, and computational genomics.

Database Management- This  requirement includes traditional relational databases which is the basis of SQL (e.g., SQL Server and Oracle). You also should know about NoSQL databases which are non-relational, distributed, open-source, and horizontally scalable (e.g., MongoDB). Finally, there are big data databases (e.g., TCGA) and big data analytics databases (e.g., Vertica) you should learn about.

Data Mining and Machine Learning- Learning techniques like hierarchical clustering and decision trees is also useful.

General Skills – There are important additional skills such as multitasking, independence, good communication skills, curiosity, analytical reasoning and managerial skills.

Free Learning Resources

Below are some free resources to start learning some of the skills you will need.

SPSS: The SPSS-Tutorials website contains a very nice tutorials.

SAS: Furthermore, SASCrunch provides a list of free resources to help you learn SAS.

Python: If you are just a beginner of python, “Bioinformatics Programming Using Python: Practical Programming for Biological Data” from O’Reilly is a good starting point. After that, you should get familiar with numpy for vectorized array computation.  scipy is also very useful for some special functions or linear algebra. If you really want to process large data, you will need to understand some of the python-C binding (e.g. SWIG, ctypes, Cython, etc.) for high performance data processing in C and manipulation in python.

R: David Romney provides a list of online resources for learning R.

Perl: Starting with the Perl online library you can access Beginning Perl or other advanced documents if you are not a beginner.

Java: There is a very good free on-line textbook for Java and the LearnJavaOnline.org Interactive Java Tutorial is also good.

Matlab: There is a great course that teaches the basics of Matlab on coursera and you can find other useful resources in this article.

Molecular Biology: There is also an interactive online tutorial in molecular biology.

Cancer Biology: Several cancer biology animations and videos are available on CancerQuest.

Genomic and genetic:  EMBL-EBI provides a free Practical course on the analysis of high-throughput sequencing data as well as another course about functional genomics.

General soft skills: hp life learning provides some very good courses.

At last, I want to tell you that your journey to be a bioinformatician won’t be easy, but it’s worth your effort and hard work. Wish you a happy journey full of excitement and knowledge.

References

  1. Vincent AT, Charette SJ. (2015). Who qualifies to be a bioinformatician? Frontiers in Genetics 6:164.
  2. Wu H, Palani A. (2015). Bioinformatics Curriculum Development and Skill Sets for Bioinformaticians. IEEE: El Paso, Tx. doi:10.1109/FIE.2015.7344321
  3. Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV. (2014). Bioinformatics Curriculum Guidelines?: Toward a Definition of Core Competencies, 10(3): e1003496.

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