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Data science in epidemiology and tutorials

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How to set up and work with Google DataLab

Step by step instructions on how to start a Google datalab project

Starting a Google datalab project takes several steps and you are well-advised to set aside an hour to get through the process and understand the mechanics of it. At the end of that session, you will get a Python based Jupyter Lab style notebook that looks like Google Collaboratory running on the google compute clusters but something you can control using your computer and terminal commands. But there is a learning curve to it and several steps that needs to be negotiated step by step. While the quickstart guide that google offers is a good guide to get you started, not all that happens is documented there, so this is more or less a pleb’s or novice’s guide to set up the process.

Step 1:

Think of a project name and an instance name. The project name can be anythig and you will need to set it up when you sign up for...

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Setting up the tools to work in Archlabs

This weekend I was working on setting up a working environment using Archlabs linux distribution for my decade old Atom processor based Acer aspire one computer. Here are the notes from the process.

What I needed to install

As I write and analyse numbers and data and work with literature files at lot, I set up my working computer with the following resources:

  1. A word processor or text processor or a text editor that can edit markdown or plain text where I can write $\LaTeX$. Archlabs came with Geany as the text editor and I use this. For code editor, it also has nano. Besides, for markdown editor I downloaded and used typora, which is cross-platform and is very useful.
  2. A document converter is very useful and I use pandoc for most of my work. This way a text file can be converted to latex, or word document with ease.
  3. Git must be installed as this helps you to talk to the world and...

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Quiz answers

Answers to the Quiz on Evidence Based Health (with answers)

Q1. Which of the following activities is the best example of evidence based health practice?

  • A heart surgeon conducted a heart transplant surgery (a surgery is an action, it is not associated with critical appraisal)
  • A university student critically appraised a journal article on an RCT of a new drug (X)
  • A lawyer presented evidence in defence of his client on medical malpractice
  • A professor lectured on the philosophical aspects of the theory of disease causation
  • An Epidemiologist conducted an investigation of a diarrhoea outbreak after a Sunday feast in a local church

Explanation: Evidence based health is essentially about critical appraisal, so this is a best example.

Q2. You have conducted a study on the association between weekly fast food consumption and prevalence of obesity among university students at the...

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Data science workflow with Jupyter and Overleaf v2, Part I: setup

Jupyter is a tool to work with data and text; Jupyter uses the markdown format to write text, and you can use markdown to write text in Jupyter and then convert the text to html and latex for outputs. If you use Pandoc, you can stretch the range of outputs to other formats (see the pandoc website for more options).

Overleaf is a webapp that uses latex to output text. Recently Overelaf released their Version 2 of the webapp; this version is still in beta; but a good feature of Overleaf’s new version is integration with github. Jupyter+Github+Overleaf provides a way to write in Jupyter, share the notebook in github where you can maintain code and show the code outputs (using binder.org), and you can share a final draft of the work and collaborate with others using a PDF document. If you use the PDF document to share your idea in the form of preprints, you can seamlessly integrate a...

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Testing testing

Google

xxx yyy aa b

A reference \cite{sss}

Ganges

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The Trouble of Conducting “Experiments” in Social Media

Caveat of What you see and Post in Facebook: Perils of Unsupervised Studies on human emotion

Kramer et al (2014) recently published an article, “Experimental Evidence of Massive Scale Emotional Contagion through social networks”, present a breach of human study ethics? Here is the link to the full text:
http://goo.gl/2vafXH

The purpose of the study was to test whether exposure to emotions led people to change their own posting behaviors. In particular, the investigators were interested to learn whether exposure to emotional content led people to post content that was consistent with the exposure—thereby testing whether exposure to verbal affective expressions leads to similar verbal expressions, a form of emotional contagion.

For this, the investigators set up two parallel experiments for positive and negative emotion: One in which exposure to friends’ positive emotional content in...

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Design Thinking

How Design Thinking Can Be Used to Address Violence Against Women

What is Design Thinking

Design Thinking refers to a process of thinking and solving problems. The process is systematic and human-centred. The process lets one come up with novel ideas, breakthroughs, and innovations to solve problems or improve situations. Design Thinking (“DT”) is oriented to human needs and emphasises users’ needs or user-driven perception of those needs. It is also a practical approach to solve problems (often known as “hands-on”, or “show, not tell” approach). Finally, DT uses metaphor based ideas – this means as we solve problems using design thinking approach, we think in metaphors. Thinking is metaphors is like thinking about events and people using references to other objects. For example, a string that connects two matchsticks would indicate a bridge (the string refers to the bridge, and the...

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