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.

Cool Techno Tips

This page will include links to cool techno tips. Comments will capture the links and the related short descriptions.

Tutorial Links

This is placeholder page for the important tutorial like sites and links for mostly Bioinformatics type sites

Least Square Analysis by dropping data points

More details will follow but the general idea is to drop data points in a random (Monte Carlo) way to detect outliers and robustness of the estimation. Instead of random drops one can compartmentelize data using tree structure to identify local mean and variation changes.

Coming Along

Plans for the site

Well for a long time I was planning the create a site where I could do the following:

  • Keep my ideas

  • Work on some projects

  • Collect opinions, ideas

  • Keep my important links

  • Keep my library or at least a link to a system that keeps my libaray

  • Have a site that would function as a research diary for each
    individual ideas, since I tend to loose the scratch papers I scribble
    them on

Now I will first start typing my ideas and ongoing work here for future use on papers. They will be password protected most of time and I will share the password with people I collaborate.. Lets see how it goes.

Testing Writely

I started using a new service called Writely. It is a web based office application with many nice ties to Blogs and Website publishing. Collaboration is also built in. I will try to figure how I can use this best.

UPDATE: I forgot to put the web link:

Orhan out.

Multi-User Desktop - Userful

Multi-User Desktop - Userful This is an interesting implementation for single PC multiple users. I still prefer using old Laptops with small linux distros specialized in remote connections and FreeNX or VNC clients connecting to a FreeNX server or VNC server. Then the only cable needed will be the ethernet cable, but still this is a cool idea.

Interesting Computer Related Links

Windows Server Hacks: Remotely Enable Remote Desktop

Concurrent Remote Desktop Sessions in Windows XP SP2

New Idea

I added a new "software I want to have" idea to my technology block. Click here to tread it :)

I want to add more over time. I have some weird ideas that someone might find interesting.

Finally I will have some time to work on my academic research as well. Expect to see the long promised filtering algorithms.

Orhan out.

Software I want II:

Over the weekend I was talking to a friend of mine and he was talking about websites where people ask for songs and song writers provide them. Basically an online music exchange. Musicians provide songs instead of goods or services and producers or singers search and buy songs...

So this gave me an idea: Do it yourself music engine...

In movies they have these artists in police stations who sketch the picture of the suspect based on the description of the observers.


There is now software police uses that does this in an computer environment. People select types of facial features and the computer merges them and then morphs the picture until the observer is satisfied. Much faster and you do not need an artist :)


There is already research in what people like in terms of melodies, rhythms etc. There are definitely winning combinations.

= Create a software where the user describes what type of music they want and the computer generates it and morphs it until the user is satisfied. User should be able to sample songs they want. Or select styles from popular songs (there should be a fingerprinting algorithm to uniquely identify a song and other algorithms that drive the work in progress towards that fingerprint (like minimization in optimization) so that they sound similarly but not the same).

Software I want: I

Okay, I have to use more than one computer at the same time most of the time. I do not want to use two keyboards two mouses etc. Yes there are hardware KVM switches that let you use multiple machines from one set of monitor, keyboard and mouse, but you still have to switch from one machine to another.

Over the years I started first with KVM switches, then I started using VNC or RDP (Microsoft Remote Desktop) to eleminate the need for extra hardware (and the other machines I use sometimes are not under my desk but far far away). Last year when I was writing some test plans I needed two displays. One for the application I was writing test plans for and one for the document. ALT+TABing was very ineffient. My work machine is an IBM Thinkpad A22. It is kind of an old machine. When you attach an external monitor to newer laptops you can display separate things on the Laptop screen and the extra monitor.. unfortunatelly A22's graphic card cannot handle such a task. So I had to give up the extra monitor but I needed more desktop real estate. So I went to the junk yard (in the office) and grabbed an even older A20. I put a basic WinXP instance on it and started looking for a way to use its screen as an extention to mine.. After googling for an hour I found Maxivista. It is a server/client software. The server part sits on my machine and the Viewer part sits on the A20. When you enable it the A20s screen becomes a second monitor on your machine. It works very nicely over the network connection. You can decide geographically where you want to put the extra screen relative to your screen and then when you move the mouse accross yours it enters the other screen. You can grab and move windows to the other screen or you can open a very large window to cover both screens (useful if you have to draw very large diagrams on Visio). So that solved some of my problems. Actually it is possible to extend the screen upto 4 machines using this software.

When I started thinking that I have finally a good solution for my problems I needed to VPN to a remote site and do some database work. My machine did not have the software and I could not install it on my machine since it was conflicting with other software. So I had to use another machine. I found the machine (another A22) but did not have space on my desk to put it. I had to put it in a folder holder behind my own A22. Of course I could not use the keyboard or the mouse stick on it. So when I was going to get a KVM switch I decided to do another Google search. After 15 minutes I found what I was looking for: A software KVM, and a free one...Synergy. It is also a client/server app. I installed the server on my machine and the client on the other A22. I configured the application with the geographic location of my machine. When I started it I had my solution...When I move the mouse up behind my own screen I moves into the other A22 with the VPN and database sofware, if I move it to the left it goes to the A20 to the left of my machine.

So know I have 3 laptops sitting on my desk. One is an extention to my screen (I do not use its CPU cycle, just the screen) and the other one is an extra CPU with its own desktop. Works very nicely.

Now what I really need is something like X in Unix, but more flexible:
-1 or more screens sharing the same desktop (like a very large screen)
-1 or more CPUs (boxes) should be running the applications on this screen. I should be able to decide where to run the application (both where on the screen and on which CPU)
-Only 1 set of keyboard and mouse.
-It should be a cross OS platform (A new virtual desktop running on Windows, Linux etc) Of course Windows apps will only run on Windows CPUs and Linux apps on Linux CPUs but both will show up on the same desktop. (Cygwin does this partially)

All the pieces are out there: Cygwin, Synergy, Maxivista etc. Someone has to bring them together. The solution would be like having a cluster on every desk. Can someone create something like that for me please????

I am back

Wow, it has been a while... finally had time and mind to write something again. Planning to go back to research again. This time with a more structured plan and time table. I finished some simulations but never had time to put them together to publish them in a meaningful way. Will start working on it soon.

Found a new toy: Amaya from W3C foundation. A very nice HTML, MATHML, SVG editor. I am mostly interested in its math representation skills. I might use it to create some short papers. I can then print them in PDF format and post online.

I will update the Technology blog with some Software wishlists. For a long time I was thinking about some software that would make my life easier... I will write them down, perhaps someone will create them for me :)

Orhan out.