uio-bmi / serverless-demo

Demo project of AWS serverless application

serverless-demo

Demo project of AWS serverless application

Application

Demo application is written in Kotlin and uses Serverless framework for enabling AWS serverless deployment. Smith–Waterman algorithm algorithm is implemented as an example:

The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the entire sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.

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Requirements

• Java 8
• Maven
• Node.js

Pre-requisites

Serverless CLI

npm install -g serverless

AWS credentials

export AWS_ACCESS_KEY_ID=<your-key-here>
export AWS_SECRET_ACCESS_KEY=<your-secret-key-here>

Build

mvn install

Deploy

sls deploy --region <your-AWS-region>

Example

Let's take as an example aligment of Hemoglobin subunit alpha and Hemoglobin subunit beta.

serverless-demo alignment: https://7zjp8jut08.execute-api.eu-north-1.amazonaws.com/dev/alignment?uniProteinId1=P69905&uniProteinId2=P68871

Execution time: 848.49 ms

Result:

CLUSTAL W MSA from BioJava

P69905    LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQV  56
          |.| .|. | | ||||  .  | | ||| |. . .| |. .|  | |||      |. .|
P68871    LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV  61

P69905    KGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPA 116
          | |||||  | .. .||.|..    . ||.||  || ||| ||.|| . |.  || |   
P68871    KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK 121

P69905    EFTPAVHASLDKFLASVSTVLTSKY 141
          |||| |.|.  | .| |.  |  ||
P68871    EFTPPVQAAYQKVVAGVANALAHKY 146

Available extra options:

Parameter	Type	Available values	Default value
gapOpenPenalty	Int		10
gapExtensionPenalty	Int		1
format	String	ALN, CLUSTALW, FASTA, GCG, MSF, PDBWEB	CLUSTALW