BeLoged

Today I was working on the blog little bit and figured out that some of the widgets are not working anymore or there is something wrong with them.

It looks like something with their javascript components went berserk. Maybe they will get fixed maybe not, but until I see changes I will not enable them. I might actually simplify things and user pure RSS feeds for most the stuff. If I can find PICASA feeds I should be perfectly fine :).

Orhan out,

Today when I was eating my Sashimi at Shogun one of the regulars who I talk to about history and Turkish language asked me about a Turkish movie he watched recently (Kurtulus Savasi).
He said in the movie any time the general ordered something the soldiers were saying “Bas Ustune” and the badly translated subtitles were saying “With Pleasure”. I explained him that it is a phrase used in military and also in the common daily language but it sounds like “Bagas Ustune” and was not sure if the “Bas” meant really head or not. Then I checked and indeed it means head. I could not find the etymological roots but will look into it again. Another example of that most people use phrases without knowing what it exactly means (Bahs Ustune?, Bagas Ustune, Bagis Ustune, Bas Ustune???). It is also funny that that I learn more about Turkish and history by talking to foreigners than talking to other Turks, maybe because when Turks talk they repeat the indoctrinated teachings and there is nothing to learn…

I am planning to create some workflow around my blog posting process. I am planning to make some entries
“live”, meaning I will start them and continue working on them. I might create an index page where I display all these entries, or even I might change the home page to be a static page displaying a welcome message, some links, and maybe a summary for newest posts. For that I might need to play with the template. Although I understand the basics behind the template file I am not sure if I am willing to spend to much time with it. We will see.

After using Wordpress on my own server for 4 years I decided it is time to move to the cloud. I have other plans for my server. At that time I liked the fact that I could upload and share papers and my code without any restrictions but today online storage is freely available and easy to configure. I can change everything about Blogger including templates to a level that it looks like it is not on Blogger. I am now trying to finish the forwarding settings for my domain on Godaddy. It does not work as “advertised” :) Need to figure out what to change exactly. So far I did the following for migration:

1. Exported content from all my other Blogspot blogs and imported them into my main blog.
2. Exported my Wordpress blog content than converted the xml file into blogger import format and imported that into my main blog.
3. Searched and found a new template.
4. Customized the new template, added some gadgets.
5. Found a javascript tool that converts some format of latex into nice equations. It works perfectly and I think it will work perfectly for what I want to do: $$ \pi=\sqrt{sample} $$

When I started blogging I wanted to be organized. I wanted to keep the information I find from different sources in a well thought manner. Well... that does not happen easily. There are too many categories things belong to, too many "one-to-many", "many-to-many" relationships. It also does not help that one day you type longer and make a good description and the other day you get lazy and only put a link, which does not make any sense 2 weeks later.
So I started looking around for a framework that would force me to be more structured. Ultimately I am planning to use this blog to keep a diary of my research. And when you do research you think of many different subjects all floating around without any solid ties to anything, but you have some idea how they might relate to other things. Writing down a sentence does not capture that soft relationship. One needs to be forced to write down all the details, so that it can be used later.
Finally 2 days ago I found something that might work: Structured Blogging plugin for Wordpress. From now on I am planning to move onto the templates for structured blogging plugin. They provide a template and force you to fill in required information. When you edit, the underlying data is well structured. The diary format turns into a database format, that can be maintained. Dividing the usefull information into bins helps a lot. When displayed it looks like a single coherent post but in the background it is a collection of sub data structures.
I will try to use it as much as possible in the future. I will post an update how things go.


Technorati Tags: StructuredBlogging

I mentioned CiteUlike before. I use it to store articles that I read or plan to read. It keeps all the relevant referencing information, links to the journals and even to the PDF if you uploaded one. This way I can access the papers I am interested in from anywhere. It is also nice to be able to search for papers by title, author, abstract etc. Sometimes you find papers by looking at other people's libraries. If they share same tastes as you do the chance that they have interesting articles is also high.

You can reach my library from this link: Orhan's library

If you are looking for cool deals on internet there are couple site people visit regularly. Apex is one I believe, also mwave and newegg are good places to start with. But this site is the best. It is a deal search engine. It comes up with multiple results for the things you are searching for, complete with coupon and rebate information. Very useful site.
Find great deals from the best websites on the newest products

An interesting approach to clustering. Minimizing the observers input and emphasizing the information content and correlations of the data.
Noam Slonim's Homepage

Wow it took me some time but I finally solved the email problem. My server does not have an smtp server and because of ISP restrictions it is a nightmare to configure one.

I used to watch black and white SciFi movies when I was a kid... well then everything was black and white since there was no color broadcast until the beginning of 80's in Turkey. I remember the old movies with simple rockets and clay monsters. It is really hard to find those movies on TV or DVD anymore. Somebody did a great job and created a free archive of all those old movies. The archive is searchable and movies can be downloaded. I definetely plan to watch some of the old SciFi movies. Here is the link...

I was searching for clusters ended up with a seasonal picture.. :) Will continue searching tomorrow...

I took this picture when I was in France last year. Why would a monster look so thoughtful?

 

 

 

I managed to get the photos show up on the site. Click on the Photos tab on the navigation bar to go to the picture album. I will continue adding more picture as time allows.

I sometimes forget that our cats were this small when we first got them. Now they are 19lb each...

There is an interesting short article in Nature discussing the gene expression levels in cells. When measurements are taken from multiple neigbouring cells one can find orders of magnitude difference between the gene expression levelsl, thus one should use geometric mean rather than arithmetic mean.
Gene expressionWhich mean do you mean? : Nature Reviews Genetics

A collection of Data Compression algorithms with nice demonstrations. Data-Compression.com

Pretty interesting site with many algorithms and their definitions. Check it out:
Dictionary of Algorithms and Data Structures

Stiched the pictures I took from the balcony manually. Still need to learn how to take this pictures so that automatic stiching works nicer.
 

I am planning to change this post regularly to capture links. I might
add them to the comments and then incorporate them into categories in
the post. The categories might change and I might need to incorporate a
different format at some point, but for now it should be enough. Please
add usefull sites into the comments and please add some detail what
that link is for.

 

 

Category	Link	Description
Search	Google	General search engine
	Google Scholar	Search for papers
	Citeseer	Search for papers and citations
	ArXiv	Search for papers
	Preview Seek	General search with categories
Bioinformatics	Protein Structures	A tutorial on protein structures
	Antimic. Peptide DB	Antimicrobial Peptide database with additional resources on design.

Research

Post to CiteULike

ThinkFree Office Online

Writely - The Web Word Processor

CiteULike: okarsligil's library

Weird Science

Global Consciousness Project -- consciousness, group consciousness, mind

On-Line Encyclopedia of Integer Sequences (Look...

Deniz Yuret's Math Problems

References

The Math Forum - Ask Dr. Math

Institute for Systems Biology: Home

San Diego Supercomputer Center: Delivering Cyberinfrastructure

MIT OpenCourseWare | OCW Home

eFunda: The Ultimate Online Reference for Engineers

Free Programming and Computer Science Books

Textbook Revolution

Welcome

Dictionary of Algorithms

Software-Tools

FileForum | TeXnicCenter

Free Source Code Version Control Software (Revision Control Software) (thefreecountry.com)

Cytoscape: Analyzing and Visualizing Biological Network Data

The BUGS Project - Bayesian inference Using Gibbs Sampling

EndNote - Introductory Tutorial for EndNote7

Xd3d home page

The Knowledgebase and Analytical Tools of Bioinformatics

Bioinformatics.Org: Molecular Linux

bioknoppix portal - Welcome to bioknoppix home

DNALinux

Bio-Linux

Paper Search

Computer and Information Science Papers CiteSeer Publications ResearchIndex

arXiv.org e-Print archive

Google Scholar

Computer and Information Science Papers CiteSeer Publications ResearchIndex

Online Articles

ACM
Queue - Hitchhiker's Guide to Biomorphic Software - Discover how
nature's most successful systems can work to inspire your software.

Bioinformatics Factsheet

To read during Protein Structure (Block 4).

Bioinformatics Introduction

How to Think Like a Computer Scientist: Learning with Python

Online Courses

MIT
OpenCourseWare | Electrical Engineering and Computer Science | 6.092
Bioinformatics and Proteomics, January (IAP) 2005 | Home

MIT OpenCourseWare | Sloan School of Management | 15.062 Data Mining, Spring 2003 | Lecture Notes

MIT OpenCourseWare | Biology | 7.012 Introduction to Biology, Fall 2004 | Video Lectures

MIT OpenCourseWare | Mathematics | 18.417 Introduction to Computational Molecular Biology, Fall 2004 | Home

MIT OpenCourseWare | Biology | 7.91J Foundations of Computational and Systems Biology, Spring 2004 | Home

Game Theory .net - Resources for Learning and Teaching Strategy for Business and Life

The Biology Project

Serafim Batzoglou's Website

cause, chance and Bayesian statistics - Bayes theory for conditional and marginal probabilities

Bayes Statistics [ISyE 8843] Home Page

Greg Butler: Bioinformatics Algorithms Course