Orhan Karsligil's Ideas, Thoughts and Collection of Resources

Noam Slonim's Homepage

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

Finally resolved the email problem

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.

Internet Archive for old Movies (Free)

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...

Clustering Techniques and Software

Resources and Links for Clustering:

Clustering Software

  • gCluto : I started testing it. It has a simple but nice data management tool set, clustering selector and a graph viewer.


Clustering Review

Iced cluster

Iced cluster

Originally uploaded by francom05.

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

Genomic Databases


General Resources

Nucleic Acids Research Database Lists contains links to many databases related to genomic data. Excellent resource. 


Antimicrobial Peptides

Antiinfective Peptides Laboratory (Trieste, Italy) 

Peptaibol Database 

Synthetic Antimicrobial Peptide Database

Antimicrobial Peptide Database from University of Nebraska Medical Center

Antimicrobial Sequences ANTIMIC


OpenCourseWare Finder

Using this site one can find all relevant Opencourseware offerings on the web. Mostly MIT courses with Reading Materials and lecture notes. Some courses have even video feeds.
OpenCourseWare Finder

Thinking Gargoyle

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




Finally have pictures on my site

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.

Edi and Budu


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

Rollyo: Roll Your Own Search Engine

Create and account, set the resources you want to search.. and type in the keywords. Search is limited to your selected sites. Might be useful for spesific scientific searches.

Rollyo: Roll Your Own Search Engine


Excellent online encyclopedia for anything related to Mathematics.

It outputs HTML/TEX/or JPEG so that the data and equations are reusable.


Global Financial Data

Financial Data from different countries for different commodities. Very useful if you need historical data.
Global Financial Data

Uri Alon's Molecular Cell Biology Lab

Interesting Articles and tools on Protein Networks and Network Motifs. Need to check the tools.

Uri Alon's Molecular Cell Biology Lab

Which mean do you mean? : Nature Reviews Genetics

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

Data-Compression Algorithms

A collection of Data Compression algorithms with nice demonstrations.

Dictionary of Algorithms and Data Structures

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

Sanibel Pictures

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

Patent 6,887,847: Antimicrobial Peptides

It is getting little crazy with Patents. People just discovering not inventing apply for patents, sometimes just to prevent others making money out of it or to sue others later.
Patent 6,887,847

New Antibacterial Peptides

Interesting story on Antimicrobial Peptides in NATURE. Recently more and more information is getting out on the design of peptides. Since in the last 40 years there are no major discoveries or R&D in Antibiotics, peptides with antimicrobial effect are becoming pretty interesting.

Link to the article:

Antimicrobial Peptides

Scientists discover how cancer spreads - Cancer -

Interesting news. Apparantly the cancer first sends a preparatory cells for the next metastasis phase. Blocking the initial wave can stop cancer from spreading. Here is the link to the article. I will try to find more information. on this.
Scientists discover how cancer spreads - Cancer -


Today I am studying different type of helices. Found an interestingly simple and clear explanation of all the molecular structures.

For years I thought the primary, secondary, tertiary and quaretenery structures explain everything. Apparantly there other intermediate structure like domains. Interesting reading. 

Useful Links

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.



General search engine

Google Scholar
Search for papers

Search for papers and citations

Search for papers

Preview Seek
General search with categories

Protein Structures
A tutorial on protein structures

Antimic. Peptide DB
Antimicrobial Peptide database
with additional resources on


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


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
Dictionary of Algorithms


FileForum | TeXnicCenter
Free Source Code Version Control Software (Revision Control Software) (
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

Paper Search

Computer and Information Science Papers CiteSeer Publications ResearchIndex e-Print archive
Google Scholar
Computer and Information Science Papers CiteSeer Publications ResearchIndex

Online Articles

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

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


Pelicans sitting in the front yard

Second full day at Sanibel Harbour Resort. The weather does not seem to
be very happy today but there are still some of these birds sitting in
the front yard :)


A day at Forth Myers

Today I woke up in Florida. It is snowing in Boston but it is 78F here. The pool outside seems very inviting. I will collect my papers and notes and will go down to the poolside soon. Will post some pictures after I come back. I am planning to use a new tool I discovered recently: Autostich. I took multiple pictures from the balcony that I am hoping to bring together to create a high resolution image.

My Glossary of Scientific Terms

This is a collection of scientific terms, phrases that are of interest to me and that need a better explanation. I will try to add links to resources and examples and extend the amount of information as time goes on.