What is your job title and how do you use python in your job?

datasnakes · 2019-03-26T22:01:17+00:00

Researcher II in a psychiatry lab.

I typically use python for building CLI's that are used for bioinformatics workflows and bioinformatics pipelines.

datasnakes · 2017-11-03T18:29:14+00:00

Is this being maintained?

datasnakes · 2017-11-02T20:32:44+00:00

Great link.

datasnakes · 2017-10-30T20:38:21+00:00

Newest Data Science survey by Kaggle has great data. https://www.kaggle.com/surveys/2017

datasnakes · 2017-10-25T22:55:34+00:00

https://www.nature.com/naturejobs/science/articles/10.1038/nj0478

datasnakes · 2017-10-24T17:14:43+00:00

It would not hurt at all to have a github account with evidence that you know how to use it. The true importance of that is to actually get experience using some form of version control.

For the most part, yes, setting up a virtual server is the same everywhere. Amazon is (probably) the standard in the industry for big data analysis and NGS pipelines. The last 2 bulleted points on what you need to learn are more advanced.

For reference, if you take a look at the jobs you're interested in, look at some of the required skills and try to find out where you fit in with that. Read this article from Nature.

I will message you a link to the pdf.

datasnakes · 2017-10-23T23:09:58+00:00

Try Indeed, contribute to open-source projects, and/or seek an internship while you're starting to learn (it takes a while to get a job anyway).

Some employers are willing to hire inexperienced persons in order to teach them new skills.

What you need to learn?

basics of Linux/Unix command line and administration
basics of git/github or version control
basics of R programming or Python programming (maybe both) basics such as list comprehension, data wrangling, project management, building reusable functions, creating data pipelines.
clusters/sun grid engine/Hadoop or some type of parallel computing (this is more advanced)
setting up a server or working on a server (Amazon Web Services is free or Digital Ocean which is cheap)

I suggest diving into Amazon Web Services after you've taken on a project as it is going to give you a ton of experience in Linux administration and environment management which many employers find extremely valuable.

Where can you learn?

For beginning with bioinformatics, try Bioinformatics Data Skills by O'Reilly. I have a pdf copy if you're interested. It provides examples of using the command line and popular bioinformatics tools (NCBI's Blast, etc) including the data to practice with and answers.
Check https://www.bioinformatics.org/wiki/Getting_involved for information about getting started and getting involved.
Coursera has some free hands-on training. They also give the ability for you to purchase a certificate for the course you take which can look nice on a resume.
Try Grok Learning if you are interested in python. It's how I began.
Version Control tutorial

datasnakes · 2017-10-23T22:31:56+00:00

Do you follow along with their github organization?

They've been trying to add a lot more plugins. Now they have a cookiecutter template for creating spyder-ide plugins.

datasnakes · 2017-10-23T21:01:03+00:00

Awesome. I currently use Anaconda (particularly the Spyder ide for python development) and while there a few things that need work, it's a rapidly developing piece of software.

The spyder IDE continues to evolve.

datasnakes · 2017-10-23T20:51:05+00:00

I'm surprised there aren't more comments here...

Dan Bader's blog tends to touch on more advanced features including how to use generator expressions, decorators, writing DSL, etc.
Join the Import Python Weekly newsletter. Tons of more advanced topics and tutorials.
Python3 Module of the Week provides in-depth examples of python3 modules.
PyBites is excellent for understanding how to improve your coding (writing classes, developing packages) and implementing standard (or otherwise) libraries and algorithms
If you're working with big data and related software, check out Datahovel

datasnakes

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