Big Talk

Some sayings that were tragic for owners although they were really intelligent. It is better sometimes to be, "Think a lot, speak less" :)

English: "Computers may just be 1.5 tons in the future"
Turkish: "Bilgisayarlar gelecekte belki sadece 1,5 ton ağırlığında olacaklar."

Popular Mechanics Journal, 1949

English: "There is no reason for any individual to have a computer in his/her home"
Turkish: "İnsanların evlerinde bilgisayar bulundurmaları için herhangi bir neden göremiyorum."

Kenneth Olsen, Digital Equipment Corp Head, 1977

Long time without post

It has been a long time until my last post except today's post. I can not beleive how the time passes so fast. What I have done; I and my ex-advisor sent our revision of the journal paper. In one of my attended course of Prof. Turkan Haliloglu, we also tried to propose a metric to differentiate native and design 3d complex structures. We submitted a kind of hybrid scoring methodology. Furthermore, with my Phd advisor, we also work on another project to detect dense modules in MIMs. Finally, we also try to code a tool named PROLiVis(PROtein protein interaction Literature Visualization).

Also, with my family, we spent one week holiday at southwest of Turkey that is a motivation for the forthcoming researches.

STRING Protein Protein Interaction Database

I am very keen on having a research over PPI networks and their visualization. Recently, I look at STRING database and I see that they have some nice visulizations using just browser api. Indeed you can also query your protein(s).

In order to have querry for the interaction visulization you just change browser adress bar text. For example,

http://string-db.org/api/image/network?identifier=4932.YML115C&
required_score=950&network_depth=2&limit=10&network_flavor=evidence

returns you


If you change the "network_depth=2" to "network_depth=3", then,

Simply you can see interaction neighborhood of any protein using correct naming and id.