Storage Considerations

NGS (Next Generation Sequencing) is a rapidly growing industry and with it has come some important challenges to overcome. One of these is the storage of the data required within this methodology. NGS inherently creates enormous amounts of data which needs to be fully and rapidly accessible. This type of data far exceeds the size of regular databases used in other applications and industries and therefore has had to be developed to suit the specific requirements of molecular biology research projects. We have teamed up with the world’s most advanced provider of such data storage systems Valex who we are working with to offer our clients the most effective storage system available for databases like ours.

YouTube Video

To find out more specifically about how BioDatomics works with data, watch the video (see left):

Valex have an established past in the field of data storage for large databases, designing the US government’s data storage and server architecture for their NGS genome projects for the NCBI. In the absence of any standards for the storage of raw NGS data, especially since the NCBI project, Valex is working hard to establish such a standard format and hopes to encourage other vendors of NGS equipment to follow suit. Our partnership with Valex ensures that our clients enjoy the convenience of not only the advanced data storage and retrieval mechanisms, but the creation of a raw data format will enhance the possibilities of collaboration and data exchange between research entities. The standardization would allow for the use of cross-platform data analysis tools – currently an unattainable prospect.

Implementation Process

For full server installation, Biodatomics would provide a chargeable service for the initial implementation phase of the software platform. This will include:
Assessment phase where we review the hardware resources required and match them with the resources available. 
Installation phase where we install the software to your server and run short tests to ensure it is running properly and correctly configured for your system.
Once everything is performing properly, we then deploy the platform and make it live for users
Ongoing administration/maintenance this is a paid service we provide so that clients can make the most of their system through the expert management of their implementation by highly knowledgable engineers. The huge amounts of data involved in a typical implementation can require careful management to ensure proper data security, integrity and backup.
The BioUML is fast developing platform so our engineers will provide whatever system updates are appropriate as soon as they are released.

Operational Information 

BioDatomics has different operational levels which would be typically assigned as follows:
Creation of new pipelines – Ph.D. Student or Post-Doctoral Fellow 
Uploading and administration of existing pipelines – Technicians and research assistants.

When new data is uploaded to the server, there is the ability to automatically update and run pipelines providing unified analysis and conserving valuable operational resources.
Hardware required
For those using the platform from a web-based interface, apart from the viewing screen size available on some devices, the system can be used from any type of web browser enabled device such as an iPad, Laptop, Desktop Computer or other tablet device. Screens on smaller devices such as cellphones are not suitable for the operation of our platform (although they will work!) but can form a handy way of showing others some visualizations or results when not at the laboratory or office. 

We have tested our software on a number of display devices and have found the optimum minimum size to make the interface ergonomically acceptable to navigate and the visual tools to be clear is a monitor capable of a minimum 1024 * 768 resolution. 

BioDatomics Data Storage

Data Collection

There are a number of methods by which BioDatomics can be populated with raw data:
Upload from a local server (available in a variety of popular formats) [link to formats section in “Features”]
Uploaded through the Web-based interface of BioUML – Online users can access files locally or remotely through the web interface for BioDatomics
Automatically abstracted from laboratory equipment.  Although BioDatomics is not currently available with lab equipment interfaces, the platform includes the requisite technology to do so. To enable the automatic acquisition of data in this manner, a script can be written (in a number of common CLI languages and a plugin can be created that will perform the data transfer as part of the available tools within the platform

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