Bioinformatics software

Automated data analysis pipelines wrapped up as easy-to-use bioinformatics software are the best option when the same analyses need to be repeated several times over time.

Bioinformatics software ensures fast turn-around times and consistent quality. We design and develop the software for you, and maintain it to provide updates and extensions.

We start a bioinformatics software project by specifying your needs, implement the pipeline using best practices, test it carefully and install it wherever you want. We train your staff to use it, and perhaps most importantly, maintain, troubleshoot and upgrade the software according to your feedback and needs. Take a look at the different steps in a common bioinformatics software project on right.

Do you want to learn more how Genevia's bioinformatics as a service works, click here to read more.

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Properly automating your bioinformatics pipeline will save you a lot of time and effort – and ensure consistent quality!

Sergei Häyrynen
Sergei Häyrynen Technology Specialist Genevia Technologies Oy

Bioinformatics software

Read more about bioinformatics software below:

  • 1) Specification
    • We start a bioinformatics software project by discussing your analysis needs to be able to propose the basic functionality of the pipeline. Once we agree on the outline, we move on to drafting the software specification requirements, defining the exact functionalities. This will be refined with you to define the bioinformatics software exactly to your requirements.

      Why?

      • To transform abstract idea into executable instructions
      • To align our expectations exactly regarding the final product
      • To identify potential pitfalls in implementation phase
  • 2) Implementation
    • We implement the analysis pipeline as a stand-alone bioinformatics software package that is fully customized to your needs from start to finish. Sky is the limit in what your new software can do, but commonly we implement some combination of the analyses that are featured in genomics, transcriptomics, epigenomics, and other data sections. Important parts of the implementation process are also finding the optimal solutions for necessary computing resources, file storage, databases and a customized user interface.

      How?

      • We use best practice analysis software as parts of the software
      • Individual pieces of software are combined with custom code (usually Python, R and shell scripts)
      • User interface can be graphical or unix command line
  • 3) Testing
    • Each component of the pipeline is thoroughly tested individually using applicable real and simulated data. The whole pipeline is then tested to ensure compatibility of components, robustness and usability. Finally, we will test the bioinformatics softaware again after installing it to its final destination.

      Why?

      • To iron out the software bugs
      • To ensure correctness of the output
      • To refine the usability of the user interface
  • 4) Installation
    • The pipeline can be run in a cloud computing environment, your own servers, with us, or locally pre-installed to hardware that we deliver with the pipeline, which ever option suits your purpose the best. If needed, we can also run the bioinformatics software for you whenever you need it (when you get a new batch of samples, for example).

      Options for installing the software:

      • The software is installed to our computing server
      • The software is installed to a cloud computing environment
      • The software is installed to your server
      • The software is installed to a dedicated computing hardware, and delivered to you

      Options for running the software:

      • We can run the software as per need basis
      • You can run the software independently
  • 5) Review
    • When the pipeline is up and running, we sit down with your staff to show what the pipeline does. We will also write a description of its functionality and instructions on how to use it.

      Why?

      • To give your staff intimate understanding of what your new bioinformatics software does
      • To train all relevant personnel to use the software
      • To enable final modifications to the user interface
  • 6) Maintenance
    • To ensure long life-span to the bioinformatics software product, we provide constant troubleshooting, add new functionalities, and provide regular updates to keep up with new best practices.

      Why?

      • The pipeline you received is a one-of-a-kind product meaning that it will require more attention than a bulk software
      • Bioinformatics is a fast developing field, and we want you to have the latest versions of databases and tools
      • As the pipeline is used, you may find more useful functionalities than those originally specified