Installing Git via Macports on Mac OSX

Tags

, ,

As I wrote more and more scripts for my work, it become difficult to keep tracking different version of my scripts for different specific tasks. Adopting a source control management (SCM) tool has been put on my agenda. An SCM tool will be even more useful if one is participating a collaborative code development project. There are many such tools available today: Subversions, Mercurial, Git, CVS, etc. I choose Git not only because it is a neat solution in terms of version control but also due to the popularity of Git-based online code development platform, GitHub. Continue reading

Building UCSC Kent Source Utilities on Rice SUG@R Cluster

Tags

, , , ,

UCSC Genome Browser website surely is one of the must-know sites for both experimental and computational biologists. As their name suggested, it is pretty nice for visualizing and analyzing genomics data without getting bogged down in bioinformatics details. You can even do quite powerful data-mining on your favorite organisms or genes by just a few clicks. A good tutorial for UCSC Genome Browser and also another powerful genome browser called Ensembl can be found here. With the nice, intuitively designed web interface in the front, what happens behind scenes is many programs or utilities being organized together and doing their jobs as integrated pipelines. These utilities (called Kent Source Utilities since they were originally written by Dr. Jim Kent) can be of great help to our own data analysis if we can have a copy of them installed on our local machine. On the UCSC Genome Browser website, they provided access to some of those most commonly used tools for stand alone use. However, this is only a subset of all their tools. If we need to use other tools, we have no choice but to build a copy of our own from their source code. This is what we gonna do in this blog. Continue reading

Parallel evolution of resistance to dauer formation in lab Caenorhabditis strains

Tags

, ,

Evolution is powerful. From a single cell, it generated the astonishing diversity of life on our planet. Yet there are also all kinds of constraints shaping evolutionary processes and limiting evolutionary possibilities. They can be genetical, developmental or physiological. So given these constraints, is it possible for evolution to take the same trajectory twice? Or let’s put it more boldly, can we even predict evolution? A recent study on the parallel evolution of dauer formation resistance in three different lab Caenorhabditis strains lends a positive answer. Continue reading

Installing Python 2.7 on the SUG@R cluster of Rice University

Tags

,

I am using a software package called Stampy to map illumina sequencing reads against the reference genome for my project. In order to install Stampy, a Python of version 2.6 or 2.7 is prerequisite. The default version of Python on our computing cluster, SUG@R, is 2.4.3 and the optional version is 3.2.1, so neither of them can work with Stampy. So I need to install Python 2.7 on SUG@R by myself. The step is as follows>> Continue reading

Equal parenting for the early stage of plant embryonic development

Tags

, , , ,

For sexual diploid organisms, the beginning of a new life is marked with the fusion of two haploid gametes (egg and sperm) from the parents. After fertilization, thousands of genes are turned on and off in harmony with exact timing and spacing, presenting a remarkable symphony of embryonic development. In animals, the zygotic genome is not expressed at first. Instead, the early stage of this process (e.g. the establishment of anterior-posterior and dorsal-ventral coordinates) is controlled by mRNA and proteins deposited in the egg cell by the mother, known as the maternal effect. By analogy, we would expect plants to follow the same rule and exhibit a comparable maternal controlled period before the activation of zygotic genome. This is indeed the current prevailing model for plant embryogenesis, according to which the maternal-to-zygotic transition should not happen until the globular stages (when the embryo has ~32 to >100 cells). Mixed evidences have been found for this model. A most noteworthy support for this model came from a recent study revealing that maternal genome contributed ~80% of the mRNA products in the early Arabidopsis embryo. In contrast, in the study we will discuss today, the authors (Nodine and Bartel) adopted a similar genomic strategy yet showed an opposite result. Continue reading

The evolution of multicellularity shown by experiment

Tags

, ,

<Note: this post will compete for the NESCent Blog Contest 2012>

All life on our planet began their incredible journeys from a single ancestral cell about three billion years ago. From this common origin, they live; they reproduce; and they evolve. Some of them stick to this single-celled form till now, yet many others chose another path: shifting from unicellularity to multicellularity. It is this crucial shift that led to the emergence of those endless forms of most beautiful and most wonderful, including our own species, Homo sapiens. Yet the impact of the evolution of multicellularity is far more than just about changing the life forms, a whole new level of biological complexity is achieved through this transition: cellular differentiation, cell-cell communication and cooperation, developmental regulation, etc. In contrast to such great importance, our current knowledge about the evolution of multicellular organisms is far from satisfactory, especially in terms of “how”, probably due to the lack of information about the intermediate forms and their habitat from fossil records. The recent study of Ratcliff et al point out an alternative way to solve this long-perplexing evolutionary mystery: studying the evolution of multicellularity by experiment. Continue reading

Hello 2012!

Tags

, ,

First of all, welcome to my blog and happy new year!

The first day of a year is always a good time to make the new year’s resolution, although personally I can seldom accomplish any of those great plans on my list. It is kind of frustrating to repeat this cycle year in and year out. So, this year, instead of making a long, detailed and ambitious list as before, I’d like to only write down one sentence: “Step out of my matchbox-like comfortable zone and explore new possibilities in my life”. Let’s see how it goes this time~ :P