Pros and cons of the professionWhere to studySalary as of 07/16/2021
A bioinformatician is a person who analyzes biomedical data. He develops and also applies algorithmic, computational and other methods that allow us to learn more about the information contained in our cells and other biological data. By the way, in 2021, the ProfGid career guidance center developed an accurate career guidance test. He himself will tell you which professions are suitable for you, and give an opinion about your personality type and intelligence.
Short description
Modern diagnostic and research methods lead to an increase in the amount of scientific data, which is very difficult to process manually. In this case, bioinformatics comes to the rescue, which as an interdisciplinary field of science was formed in the second half of the 20th century. Bioinformaticians use elements of applied mathematics, statistics, and computer science. During their work, they operate with the following knowledge:
- programming languages, mainly Java, C, C++, C#, R;
- HTML markup language;
- programs: ACT, BLAST, Clustal and others;
- SQL, CUDA.
Let's look at the main areas of research:
- genetic sequence analysis, evolutionary computational biology;
- assessment of biological diversity, annotation of genomes.
The profession is young, and in the future it will develop even more rapidly, because the use of computational methods guarantees high accuracy, speed and eliminates the human factor. Bioinformatics technologies are needed in biochemistry, biophysics, ecology, pharmacology, agriculture, genetics and other fields.
Someone has already done this. So find them and ask!
No matter how tricky the problem is or how new the method is, there is always a chance that people have already dealt with what you had to deal with.
There are two sites where problems encountered in research are discussed - BioStars and SeqAnswers (and purely programming questions - Stack Overflow). Sometimes you can get good advice even on Twitter. Search the Internet to see who is working on similar issues in this country and in the world and contact them (see Table 3). Table 3. Russian “dry” laboratories.
| Laboratory | City | What do they do |
| Molecular Modeling Group at the Faculty of Biology of Moscow State University | Moscow | Molecular dynamics of proteins and peptides |
| Group of Computational Structural Biology, Bioinformatics Group and Laboratory of Evolutionary Genomics at the Faculty of Bioengineering and Bioinformatics of Moscow State University | Moscow |
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| Laboratory of Chemical Cybernetics and Computer Molecular Design Group at the Faculty of Chemistry of Moscow State University | Moscow |
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| Laboratory of Biocatalysis and Biotransformations and Department of Mathematical Methods in Biology, Research Institute of Physico-Chemical Biology, Moscow State University | Moscow |
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| Laboratory for Modeling Biomolecular Systems at the Institute of Bioorganic Chemistry RAS | Moscow | Molecular modeling of biomembranes and membrane proteins, as well as biologically active substances |
| Laboratory of Structural Bioinformatics and Structural-Functional Drug Design at the Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences | Moscow | Computer modeling of protein complexes with proteins and drugs, drug design, pharmacology, study of structure-activity relationships |
| Educational-Scientific and several other bioinformatics groups at the Institute of Information Transmission Problems of the Russian Academy of Sciences | Moscow | Systems biology, analysis of spatial structures of biomolecules, comparative genomics. Organized by the Moscow Bioinformatics Seminar, the Moscow School of Bioinformatics and the Moscow Conference for Molecular Computational Biology. |
| Laboratory of Systems Biology and Computational Genetics and Bioinformatics Group at the Institute of General Genetics of the Russian Academy of Sciences | Moscow | Search for functional motifs (transcription factor binding sites, etc.) in DNA sequences |
| Laboratory of Bioinformatics and Systems Biology at the Institute of Molecular Biology RAS | Moscow | Methods of bioinformatics and search for functional motifs, prediction of susceptibility to diseases |
| Laboratory of Bioinformatics at the Research Institute of Physicochemical Medicine | Moscow | Problems of metagenomics and proteomics |
| Laboratory of Algorithmic Biology of the Academic University of the Russian Academy of Sciences | Saint Petersburg | Problems of “assembly” and analysis of genomes |
| Laboratory "Algorithms for assembling genomic sequences" of the National Research University of Information Technologies, Mechanics and Optics | Saint Petersburg | Problems of “assembly” and analysis of genomes |
| Group of Bioinformatics and Functional Genomics of the Institute of Cytology RAS | Saint Petersburg | Exploring the functional significance of overall genome structure |
| Laboratory of Functional Genomics and Cellular Stress and Mechanisms of Cell Genome Functioning, Institute of Cell Biophysics, Russian Academy of Sciences | Pushchino |
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| Laboratory of Applied Mathematics at the Institute of Mathematical Problems of Biology RAS | Pushchino | RNA secondary structure, alternative splicing |
| Laboratory of Protein Physics, Institute of Protein, Russian Academy of Sciences | Pushchino | Theoretical and experimental study of the folding processes of protein molecules |
| Department of Systems Biology, Institute of Cytology and Genetics SB RAS | Novosibirsk | Postgenomic bioinformatics. Computer analysis and modeling of molecular genetic systems. Gene networks. Models of the evolution of microorganisms. |
| Group of the Laboratory of Environmental Biochemistry of the Institute of Biology KarRC RAS | Petrozavodsk | Molecular modeling of biomembranes |
| We are aware that it is impossible to list all worthwhile scientific groups in one table. If we have forgotten someone, we will be happy to add them. The table was prepared by Elena Chuklina (Moscow Institute of Physics and Technology / Educational and Scientific Institute of Information Transmission Problems of the Russian Academy of Sciences). | ||
To top it off, we can say that there are a lot of forums and user groups on the Internet where you can ask questions. Install Linux and start learning something bioinformatics online. With the right amount of perseverance, you will be surprised how much you can achieve with just a computer and Internet access!
The article was written based on an essay in the journal Nature Biotechnology [10] with the participation of Arthur Zalevsky and Elena Chuklina.
The author of this note pretends to simulate on a computer the interaction of the ligand-binding domain of the nicotinic acetylcholine receptor type α7 with one of the natural neuromodulators.
Features of the profession
Bioinformatics is at the intersection of medicine, biology, applied mathematics, and computer science. The responsibilities of people who choose this direction include solving global problems:
- search for methods of treating oncological, chronic, autoimmune diseases;
- extending the life span of the population, improving the environmental situation, searching for the longevity genome;
- development, planning, implementation of mathematical methods, algorithms, programs used for the analysis of medical and biological information;
- application of the obtained results in practice.
The areas of research are vast and bioinformatics has enormous potential. The international labor market is already experiencing a shortage of bioinformaticians, because both pharmaceutical and IT companies are interested in them.
Of course, a bioinformatician must have impeccable knowledge in the field of medicine and biology, understand complex professional terms; knowledge of the English language will be a huge plus. Experts in this field spend most of their working time at the computer; the work is sedentary, but has enormous social significance.
Pros and cons of the profession
pros
- A very promising field of activity. The growth of data sets will lead to even greater demand for bioinformaticians.
- From year to year, there has been a steady increase in wages in this segment.
- All doors are open to bioinformaticians - from domestic research centers to respectable global IT companies.
- For their work, mathematical methods and computer programs are used, so bioinformaticians do not interact with patients or biological materials.
- Knowledge of programming languages and the fundamentals of applied mathematics allows a bioinformatician to choose a different segment of activity. For example, classical programming, program development and testing.
- Constant self-development and improvement of professional skills.
- The opportunity to analyze data sets, knowing that the results of the work will save the lives of thousands of people in the future.
- Bioinformatics research areas receive active government support.
Minuses
- Sedentary work is associated with increased brain activity.
- The profession is more suitable for people with a technical mind.
- Young bioinformaticians with no work experience may have problems finding employment.
- Some doctors are distrustful of this interdisciplinary field.
Bioinformatics training
Universities
Moscow State University named after M.V. Lomonosov
Bioengineering and bioinformatics (Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University)
First Moscow State Medical University named after. I.M.Sechenova
Bioengineering and bioinformatics (I.M. Sechenov First Moscow State Medical University)
Bioinformatics is just gaining popularity, but specialized faculties are already functioning successfully in Russian universities. If you want to become an expert in this field, then pay attention to the direction of training “Bioengineering and Bioinformatics” (code: 05/06/01).
To enter this specialty, you must pass the Unified State Exam in specialized mathematics, as well as the compulsory Russian language. The remaining exams depend on the university, but most often these are biology, chemistry, physics or computer science (1-2 of those listed). Few Russian universities train personnel in this area, and the passing score for the subject is 64-92, with no more budget places 30. Form of study - full-time, duration - 5 years (specialty).
Use version control
Using version control will allow you to more flexibly manage code development, make it easy to return to previous editions of the program or switch between different branches of development, and also open up the possibility of joint program development.
Common systems - such as Git or Subversion - will make it possible to easily publish a project on the Internet. You will do better for yourself, first of all, if you are not too lazy to write several clear README files and put them in the right places in the project; this will help you tremendously if months or even years later you have to go back to your old program. Document programs and scripts so that it is clear what they do. When publishing a scientific paper, it is a good idea to also publish the original programs that were used to calculate the data: this will allow others to use the same method and reproduce your results. It would also be a good idea to keep an electronic diary in which the entire progress of the work would be recorded. Online repositories such as Github allow you to do this, and will also allow you to store working versions of the program, which will provide an additional layer of backup for your work (see Table 1). Table 1. Important tools for a computational biologist.
| Task | Tools |
| Joint program development | Make your code (and possibly data) available online through online repositories like Github, Sourceforge, or Bitbucket. There are many tutorials on the Internet on how to use these systems. There are also scientific project management systems, which are described in a separate sidebar. |
| For complex tasks write scripts and pipelines | To do this, you can use both modern developments, like Ruffus, and time-tested classic UNIX utilities like Make. The choice of specific tools depends on personal preferences and favorite programming language |
| Make your pipelines accessible | It's possible that you're at ease on the command line, but most of your colleagues probably aren't. The pipelines you create can be equipped with graphical interfaces using the Galaxy or Taverna systems. |
| Developer Tools (IDE) | Of course, you can write programs in any text editor, starting with , but it will be better if you master more advanced tools - such as the Emacs text editor or a full-featured development environment like Eclipse. And, again, the specific choice will be based on your preferences and favorite programming language. |
Project management systems
Another useful tool, in addition to version control systems, that can be borrowed from programming practice is project management systems. It's easiest to think of them as an advanced e-zine that gives you the following additional features:
- Creating and assigning tasks. For example, “count this and that.” Within a task, you can have discussions that will be conveniently structured and will not turn your mail into a warehouse of terrifying correspondence like “Re: Project X (100).” However, you can set up mail notifications, so no one will miss an important comment.
- Attach and organize files with detailed descriptions and version support a la Dropbox. Have you ever had to search for a long time in several threads of correspondence on a project for any files with obscure names, like “report_ACC_clean.xxx”?
- In the built-in Wiki, you can enter descriptions of program launch procedures , experimental methods, embed videos, and even render LaTeX formulas.
- Text search across all content , including attached files.
- Integration with version control systems for software development allows you to conveniently correlate tasks with changes in repositories.
- There are even such exotic features as organizing your own Google Docs analogue for simultaneous text editing. Not all information can be trusted to third-party resources.
In our laboratory we use Redmine - this is an excellent open source project management system with many plugins. You can deploy it yourself or rent a virtual machine with an already installed system. The most famous proprietary alternative is Basecamp.
Zalevsky Arthur , Faculty of Bioengineering and Bioinformatics, Moscow State University (computational structural biology group).
