May 2, 2017

FAQ

Frequently asked questions

Exact matches only
Search in title
Search in content
Search in posts
Search in pages
Filter by Categories
cost
License
Uncategorized

 

Is the eBioKit distributed as Open Source software?

All software tools and data included in eBioKit are open source and free to use. In addition, the eBioKit web interface and included tutorials are also open source and under Creative Commons Attribution (CC BY) license.

Can I download an eBioKit?

Currently, the eBioKit is not available as a downloadable resource for being too large (6-7 TB), and its acquisition must be done through the developers team, who will seek the way to get a copy of eBioKit that best suits your conditions.

How much cost an eBioKit?

The eBioKit is distributed at no cost, except those derived from the purchase of the necessary hardware to run the system (i.e. the Mac mini or Mac pro machines) and transportation.

Performance of the system

The version of the eBioKit built on Apple Mac Mini machines with 16GB of RAM has been successfully used for courses with up to 25 students working in parallel on the tutorials included in the platform. This version may not be recommended for large NGS analysis work. On the other hand, the Mac Pro based version with 32 GB RAM allows up to 40 students to attend to a course and work simultaneously. In spite of the system has not been benchmarked for intensive work yet, it is know that the system is routinely used as an analytical resource by some of the project partners.

How can I update my eBioKit?

Updating services in the eBioKit potentially has two obstacles: the first and most obvious is the limitation imposed by the poor quality of the internet connection in those places for which the system has been mainly designed that makes almost impossible to download the large amounts of data that would be necessary for the upgrading. The second hurdle is to maintain the consistency of the system so that the update of the services does not limit the ability to complete without problems the tutorials included.

So far, the strategy followed has been the periodic production of improved versions of the system including updates of the installed services and their corresponding tutorials. The distribution of these new versions depends on the infrastructures of the center or university that wants to update its eBioKit. In certain cases, it has being possible to distribute images of the new versions through the internet. However the ability to transmit several terabytes without problems is hampered in most African countries by failures in the electric power or in the internet connection. Alternatively, most updates have been made “in situ”, for example, taking advantage of a visit to the host centre or university and making a copy of an updated version of the system. This method has been possible thanks to by the great participation of our group in research and sustainability projects in Africa, Asia, Europe and the Americas and based on necessities of numerous courses organized there. Nevertheless, we consider essential the search for a more sustainable system for updating the eBioKit and for that reason we are currently working on a new architecture based on Dockers that allows keeping the system up-to-date by selective updating of services through internet, which will potentially avoid unnecessary displacements and minimize the data transfer. We are also, in parallel, working on a model based on the distribution of hard drives containing yearly updates.

About eBioKit team

People that have worked on the eBioKit project in chronological order:

  • Alvaro Martinez Barrio
  • Erik Lagercrantz
  • Fei Fei Xu
  • Martin Norling
  • Oscar Eriksson
  • Rafael Hern├índez de Diego

Project leader:

  • Erik Bongcam-Rudloff