Monday, 25 February 2013 at 8:03 pm

Just discovered this crowd-funding site for scientific research: https://www.microryza.com/

It's an extremely cool idea that gives a bit of power to the public in steering the direction of research and at the same time act as scientific outreach. It also allows undergraduate or graduate students to have some extra money for reagents or equipment in addition to being a great platform for communicating their projects.

I do have a few questions that doesn't seem to be clarified on the website:

• What criteria does the site use to approve proposals?
• What is really the incentive for public to donate money? For example, Kickstarter gives rewards for donations.
• How does academic institutions view this source of money? The site says money is given officially as "gifts" to the academic institution and put under the researcher's project budget.
• Does this only work for US institutions currently?

Looks like a potentially good platform to crowdfund some sequencing projects...

Sunday, 10 February 2013 at 1:24 pm

There has been a lot of heated discussion on what exactly the role of the bioinformatics is and what contributions it has made to biological sciences. The discussion started with the re-discovery of Fred Ross's farewell to bioinformatics blog entry posted mid last year, in which he used many colorful words to describe the inadequacies of the field. And from there, it was posted on several biology, bioinformatics, and programming news aggregator sites (This post on BioStar tracks the discussions), sparking debates.

I can't claim to be very experienced in the bioinformatics field. I am currently still trying finish my phd. However, I have been a hobbyist programmer for quite a while now and I've also got a decent amount of experience in academia as a lab technician, out-sourced programmer, lab manager, and grad student.

So here is my two-cents on this discussion.

Monday, 04 February 2013 at 3:18 pm

For phd students currently writing their thesis/dissertation, try out sharelatex.com. It automatically saves and allows you to compile on the fly and view the resulting .pdf. Here is a pretty standard latex template for any report type document:

\documentclass{report}\usepackage[utf8]{inputenc}\usepackage{natbib}\usepackage{graphicx}
\title{my thesis}\author{my name}\date{my date}
\setcounter{secnumdepth}{5}\begin{document}\tableofcontents
\chapter{Introduction}\section{Organism X biology}\subsection{Life cycle}\subsubsection{Phase 1}My text content\subsubsection{Phase 2} My text content
\section{Organism X bioinformatics}\subsection{Available Data}\subsubsection{Genome}My text content\subsubsection{Transcriptome} My text content
\chapter{Organism X genome assembly}\section{Section}
\chapter{Conclusion}\section{Section}\bibliographystyle{plain}\bibliography{references}\end{document}

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