Blog for 2010-06-06

From BioDivBorneo2010

Jump to: navigation, search

Romadoni Anggoro

Today was the first computer day. The class was started with introduction to open source platform including open source software. Open source have two meaning. First is free, we don't have to pay any money to get the software. Second, the source code is open so the user could modify and redistributed the software.

The others benefit of open source are supported by large community. So if we find any bugs or any problem, we can report. Mostly they will respond quickly.

One of open source platform is GNU Linux or normally we call Linux. Linux is using UNIX, same with apple but free. For office software, there are open office and neo office available. These two software have a complete package for office computation. For graphic work open source has Inkscape (vector editor) and GIMP (photo editor).

We installed many software for bioinformatic demand. The software ware:

1. Open office	
2. Jabref             ->  for bibliografi
3. Mosquite           ->  species determination
4. R and some package ->  statistic	

and R. R is a complete statistic software. It run in command line. We worked on data from our group measurement and ctfs data. Before worked in R, we choosed the right directory to work. Also make sure that the data was in the same folder. Here are the step:

  • save as the data format into .csv. for example group4.csv
group4<-read.table("lambir2912.dat",header=T,sep="|")
group4$dbh<-group4$girth/3.1415 
ctfs<-read.table("lambir2912.dat",header=T,sep="|",na.strings=".") 
colnames(ctfs)<-c("tag","dbh","sp")
new<-merge(ctfs,group4,by="tag") 
new$growth<-new$dbh.y-new$dbh.x 
mean(new$growth,na.rm=T) 
q()

This produce mean of growth each tree.