How do I design a biological database

Question

[Mac]

Hello, My lab is doing a lot of NGS sequencing, but the way the sequences are are documented makes it difficult to retrieve them or keep track of the data. I would like to create a database that has the following features: -A Graphical user interface and can also allow one to upload/retrieve sequences, and can incorporate links to quickly BLAST or analyse the sequences with other online tools.
-allows one to access it in the command line -that has another section that has records of what's in the lab, what needs to be ordered etc. -that is also secure.

I wanted to know an easy way to do this as I have never designed a database. Are there general database templates I can adopt and modify to suit my lab needs?

Thank you!

[GenoMax]

Sounds to me like you are looking for an integrated LIMS/e-notebook type solution. Take a look at several open source projects available from Babraham Bioinformatics group that would partially fit the bill. You would be best off having access to minimal IT support to implement one or more of these.

[John]

+1 for Babraham software for this. I have used Labrador in the past and found it very nice (http://www.bioinformatics.babraham.ac.uk/projects/labrador/)

There's also an excellent project by a colleague of mine called DeepBlue which would also be a very good fit: http://deepblue.mpi-inf.mpg.de/

[Mac]

Thank you both options are very interesting. For the DeepBlue Epigenomic dataserver is there an option to store the data on our servers instead?

[John]

yes, absolutely - in fact i'm sure if you send him an e-mail he'd be happy to help you set it up - http://pih.bio.br/

Answer 1

[WouterDeCoster]

I think your plans for the database are a 'bit' broad. Why would your database have that many purposes? You may also want to specify what is 'a lot of sequencing' in terms of experiments and/or storage space.

[Mac]

NGS sequencing. The primary purpose is for storing and retrieving biological sequences. 10 TB storage space

Answer 2

[Echo]

store the file in file system and keep the information in database is better. or just a txt or json file.

write several script to handle the cmd needs.

for web interface, you can write script to generate html file include the link to download.

for small lab, usually, the project change very quickly. it is just a waste of time to create UI.