MySQL is good choice for a small sized genomics research project
December 21, 2018

MySQL is good choice for a small sized genomics research project

Anonymous | TrustRadius Reviewer
Score 9 out of 10
Vetted Review
Verified User

Overall Satisfaction with MySQL

My company is a healthcare delivery institute and performs a number of data science projects collaboratively with other healthcare, research, and academic organizations. We conducted a genomics research project that stores sequencing data with attributes of miRNA, exon, intron, Methylation, etc into a relational database and developed a web based visualization tool presenting patterns based on the data in the database. In the project, we used MySQL database for storing genomics information.
  • It’s available for free but provides a lot of functionality even for a free database engine. There are tons of knowledge sources out there in case we needed technical support and dealt with troubles.
  • Since our project was a genomics project, we handled tables with numerous rows (e.g. sequencing). MySQL is very stable and performing well in hard conditions.
  • There are many developers who are familiar with MySQL already, like other major RDBMS products. It is easy to hire engineers with reasonable payment.
  • MySQL doesn't provide good data wrangling functionalities, such as parsing JSON or XML. We had to transform them outside MySQL on the web application server side using JSP.
  • As we move forward to adopt more genomics information, MySQL may lack of dealing with "big data" functionalities.
  • It is a freely available S/W and easy to manage budget, but there are possibilities to spend cost for additional technical support.
  • There is few negative impact of using MySQL, at least in terms of adoption cost. It is free for use.
  • From workforce management perspective, it is easy to predict budget since many developers are familiar with the product. We don't need "special" developer for MySQL which cause uncertainty of salary for the specialty.
  • MySQL runs well with any operating systems and that's one aspect that the product is easy to be adopted.
We have used Oracle as our clinical databases that stores patient records. In this project we didn't used Oracle but separately built MySQL based data infrastructure as this is an independent scientific research project. Oracle is great overall, with most of functionalities needed and good performance, but it is heavy and expensive. MySQL is lightweight and well aligned with a small scientific research. Still an Oracle based tool such as SQL developer can be used with MySQL well. There was very few issue with running two different databases but make them connected and harmonized.
MySQL is basically a very well known, guaranteed relational database with minimum risk of adoption and use. Which means, for any general purpose MySQL database will fit in to some extent. Especially since it is free for use and doesn't come with burden of budgets. In our project the problem was extensibility to larger scaled genomics information, that may require big data management functions. MySQL is okay when it is small project, but as it grows, other products like MongoDB should be considered.