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How do I design a biological database

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!

sequencing
• 3,561 views • link
updated by Echo Echo • written by Mac • Mac

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.

• 1 views • link
written by GenoMax GenoMax

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

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written by Mac • Mac

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/

• 1 views • link
written by John John

2 answers

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.

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written by WouterDeCoster WouterDeCoster

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

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written by Mac • Mac

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.

• 1 views • link
written by Echo Echo

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