Bioinformatics software

Automated data analysis pipelines in the form of easy-to-use bioinformatics software are the best option when the same analyses need to be repeated over time.

Bioinformatics software ensures faster turnaround times and consistent quality. We design and develop the software for you, and maintain it, providing updates and extensions.

We begin a bioinformatics software project by specifying your needs, implementing the pipeline using best practices, testing it carefully and installing it wherever you want. We train your staff to use it and, perhaps most importantly, maintain, troubleshoot and upgrade the software in accordance with your feedback and needs. Take a look at the different steps involved in a typical bioinformatics software project on the right.

To learn more about how Genevia's bioinformatics as a service (BaaS) 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 Project Manager, Technology Specialist Genevia Technologies Oy

Bioinformatics software

Read more about bioinformatics software below:

  • 1) Specification Good planning is the key to successful software development
    • We begin a bioinformatics software project by discussing your analysis needs in order to be able to propose the basic functionality of the pipeline. Once we have agreed on the outline, we move on to drafting the software specification requirements and defining the exact functionalities. This will be refined in collaboration with you in order to fine-tune the bioinformatics software to your exact requirements.

      Why?

      • To transform abstract ideas into executable instructions
      • To accurately align our expectations regarding the final product
      • To identify potential pitfalls in the implementation phase
  • 2) Implementation Tailored software development leveraging publicly available tools
    • We implement the analysis pipeline as a stand-alone bioinformatics software package that is fully customized to your needs from start to finish. The "sky is the limit" regarding the features that your new software can have, but typically we implement a combination of analyses that are featured in the Genomics, Transcriptomics, Epigenomics, and Other Data sections of our website. Key elements of the implementation process are also identifying optimal solutions for the necessary computing resources, file storage, databases and a customized user interface.

      How?

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

      Why?

      • To iron out any software bugs
      • To ensure correctness of the output
      • To optimize the usability of the user interface
  • 4) Installation Your server, our server, the cloud — whichever is most convenient
    • 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, whichever option best suits your needs. If necessary, 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 on a cloud computing environment
      • The software is installed on your server
      • The software is installed on a dedicated computing hardware, and delivered to you

      Options for running the software:

      • We can run the software on an as-per-need basis
      • You can run the software independently
  • 5) Review We will make sure you know how to use the software
    • When the pipeline is up and running, we sit down with your staff and demonstrate what the pipeline does. We also prepare 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 We will add new functionalities for as long as you want
    • To ensure the long life-span of the bioinformatics software product, we provide constant troubleshooting, add new functionalities, and provide regular updates in order 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 an off-the-self-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 a need for different functionalities than those originally specified