PopSim.py

Script wrote to simulate population evolution under genetic drift and natural spontaneous mutation only using simulated microsatellite data.

Quotes from A Byte of Python

There are two ways of constructing a software design: one way is to make it so simple that there are obviously no deficiencies; the other is to make it so complicated that there are no obvious deficiencies.

— C. A. R. Hoare

Success in life is a matter not so much of talent and opportunity as of concentration and perseverance.

— C. W. Wendte

Build a bioinformatics lab server with a tight budget (Part1)

A friend of mine is going to set up a plant pathology lab soon, and he is planning working with some bioinformatics work over there. I am helping him build a lab server with a reasonable price, which in this case was USD1.5k. I plan to use this opportunity to write a blog to document the whole process to share with the potential community.

Nowadays, next generation sequencing (NGS) is becoming affordable and approachable to most of the labs. Although many other options are out there for people who want to seek for data computing solutions. But the cheap way for a lab with limited fundings could be a lab-owned server. Now let’s see what we can get with this price, and what’s the performance is gonna be.

1. Consult for the scope of their research. 

At this step, I had a couple of conversation with my friend, who is a pure molecular bacteriologist with limited experience in bioinformatics. From the conversations, I understood the potential applications in his research, and the size of the potential computation loads. After a few rounds of conversation, his requirements and applications are listed below:

  • Bacterial genome assembly
  • Comparative genomics
  • Transcriptomics with emphasis on genes DE analysis
  • Genomic features annotations

Based on the requirement, I made a few suggestions on the configuration of the server. First, due to the small size of bacterial genome, the storage of the server is not the first of concern.

Blog officially moved to wangjie.esy.es

Blog officially move to this new site. Even though I haven’t updated this blog for a long time, hopefully I can continue to write something new about my research and science.

In the meantime, I will make some comments to the tools we commonly used in our lab in order to appeal for the awareness of some problems from the end users like me.

That’s what I have for today, I will start my new post very soon. ^_^.

 

-J

The most common NGS assembler

genome_assembly_survey_results

Survey did by Keith Bradnam

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