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Team Name: Team Reetu and Friends

Members: Reetu Tuteja, Jennen Maryniak, Erika Tapia, Hayden Dunn, Andy Garcia, Nick Reppe, Jiatian Wang

Deliverables

  • Critical
    • Optimize the current version of SequenceServer to support a class of up to 100 individuals without throttling.
    • Lower average run time of engine.
    • Ability to create custom blast databases
  • Nice-to-haves
    • Update UI
    • Cache repeated query

Project Delivery:

    • Docker
      • Technology requirements: A computer and the Docker installed on the machine.

      • Potential unknowns and problems: Most individuals of the group have not yet learned how to use Docker.

      • Weaknesses: New to group, could be chaotic to use.

      • Strengths: Docker is incorporated in BLAST

    • Github
      • Technology requirements: A computer and an account affiliated with Github.

      • Potential unknowns and problems:  Not everyone has used Github and may lack knowledge in using this tool.

      • Weaknesses: Could be a weaker presentation vs other tools.

      • Strengths: Organizes everything really well. It can help the client go through our portion of the project.

List of questions:

  1. Is the current version of SequenceServer running a submitted job sequentially or using some method to parallelize it?

  2. How does he plan to control the large queries/database searches? Do we have to create login authentication for users?

Development Process:

For now, we will be using Google Drives to share project progression throughout this assignment as well as Slack. We are looking towards learning Agile to better our visuals throughout the course as well as TRELLO, but Google Docs, Google Drives, etc will suffice for the time being during this period for the project. We are capable of adapting to new systems if need be.

Learn what BLAST has to offer concerning our deliverables. Can we use all or some of their tools? Does what they have work with SequenceServer and can we make them work with other applications?

Learn more about distributed computing and how it relates directly to BLAST.

 

The Plan:

1) Learn all concepts necessary to assist our client. I.E. Docker, SequenceServer, makeflow, distributed computing.

2) Use the concept of distributed computing to, hopefully, provide solutions or new perspectives for our client.

3) Using this tool, test job prioritization.

4) Run multiple queries and record benchmarks.

5) Record all data and use Docker to finalize.

 

Creating an image with Atmosphere

Open the Request Form

  1. Click Projects on the menu bar and open the project with the instance to use for the new image.
  2. Click the instance name. The instance must be in Active status.
  3. In the Actions list on the right, click Image.

Image Info

  1. Select tags to add to your image
    1. In our case, we have “ABBlast”, “Base”, “nodesktop”, “nogui”, “Ubuntu”, “ubuntu1804”
  2. Click Next

Version Info

  1. In New Version Name, enter the new name or number of the tool to distinguish this tool from others with a similar name
    1. Ours was “seqserver_RT”
  2. Click Next

Privacy

  1. Select the visibility level for the image from the dropdown list:
    1. We chose “Public”
  2. Click Submit

Review

  1. Verify that the options you selected are correct.
  2. Click Request Image. You will receive an image from Support when your image is ready.

 

Benchmarking:


DNA sequence length

Time (sec)

Small database (2,291 Mbp)

Time (sec)

Large database (64,036 Mbp)

1 kbp2.9653.13
2 kbp3.95111.54
5 kbp4.89158.5
15 kbp14.01304.88
30 kbp31.961206.92

 

 

No. of protein sequences

Time (sec)

1 core instance

Time (sec)

8 cores instance

13.450.69
58.160.89
103.451.1
50578.526.15
1001532.98666719.18
5006851.48610.11

Conclusions: We ran sequence server on same set of sequences and database on 1 core and 8 core atmosphere instances. We observed a significant decrease in time taken to run the query when used an 8 core instance compared to 1 core.

Concept Map:


https://drive.google.com/file/d/1zl4DriHKgofOHN1irYLx9pAq9nZMd24O/view?usp=sharing

 

 

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