Since I’ve been doing research for my master, I have to spend lots of time reading journal and conference papers. The problem is organizing these papers. I did a little research to find some ways to automate the tedious task of downloading paper,organizing by author,date,conference and so on. I found some tools which are Zotero It is a good citation tool which is multiplatform and can synchronize your library across your machines. The free account only offers 300 MB webstorage. That’s the only problem I found and I starts with Zotero. Mendeley Mendley is the tool I jumped after I run ou...

I read an article about a guy’s concept of making his digital devices to minimalize for the sake of keeping his mind and work-flow simple and straightforward. After I read that, I forgot to keep a bookmark this page and couldn’t find it again. The devices he have are iPad and iPhone. It’s so simple. He keeps the springboard of both his devices “blank”. That’s it. One thing I still remembers what he replies to others who ask what if you don’t know the name of the application you are looking for. He said “If you doesn’t remember the name of the application you use, it is not important o...

It s the buzz word in web-design,“minimalism”. What if your life minimize to a certain ratio? What if you reduces your desires and becomes anti-consumerism? It follows the teaching of Buddha too. However,people likes to have newest,most expensive,the rarest possessions on their hands. To live a pure unselfish life, one must count nothing as one’s own in the midst of abundance. The question is do you need all of these belongings? Do your life needs to carry all these stuffs with you? Most people thinks having expensive clothings,fastest car and latest techie promises Happiness. Ho...

Well…It’s another random thing I am working on. As you may or may not know, the size of the DNA raw sequence is quite huge. It’s at least 1 GB and some files are around 25 GB. When I am pre-processing these data-sets, it generates more files which are at least 3x bigger than the original file. What happen is that I run out of storage in sever even though it still has like 80 GB free space left. However, that’s not enough for a 25 GB sra file to split into single-ended file. So,my supervisor told me to map a network storage or find a solution to solve. Ok.I did some light research about N...

This week, I have to analyze and trim the adaptor sequence for 5 illumina HiSeq 2000 reads (Penaeus_monodon & Litopenaeus vannamei species). If you want to know about the research work I am helping with,please go to this page: CentexShrimp. Ok….Back to Sequence Trimming, The detail information about the run sequence can be viewed at NCBI Website. SRR346404 SRR653437 SRR388207 SRR388221 SRR388222 This is the list of the tools I used. sra tool Kits : contain several tools for converting datasets from one format to another. for this analysis, I convert the sra dataset...

This is the pipeline process for 454 sequencing. I am not a biotech guy but after spending time, giving effort and getting help from my collague, I came up with a way to do that. The tools I used are NCBI SRA Toolkit and 454 sequencing tool for multiplexing. process Downloaded SRA files from … Converted these SRA files into SFF format using sff-dump tool $ sff-dump -A xxxx.sra Rebuilt the scores of converted sff dataset with sfffile tool $ sfffile -o xxxxxxn.sfff xxxxx.sff Split the file according to MID groupname $ sfffile -s ...

Well, It is not a choice. I have to work on Linux platform since I joined a part time job at biotech gene annotation lab. Now,the website was settled and development is done. The researcher told me to analyze DNA sequence datasets and blah blah… So,Ubuntu becomes my home because most of bioinformatics tool are Linux binary applications. Let’s say around 6 months, this Linux distro fails me 3 times. Even though it said “Ubuntu 12.04 LTS(Long Term Support)”. You should call it as “Long Time to Stable”. Anyway,I have to use it and I try to find the best applications. Here is the list for nex...