BeLOGED

Asked at Lunch

2009-09-15T14:44:00.008-04:00

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…

Ideas about my Blog

2009-09-15T14:13:00.003-04:00

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.

Finally blog migrated

2009-09-15T14:08:00.004-04:00

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:

Exported content from all my other Blogspot blogs and imported them into my main blog.
Exported my Wordpress blog content than converted the xml file into blogger import format and imported that into my main blog.
Searched and found a new template.
Customized the new template, added some gadgets.
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: $$ \pi=\sqrt{sample} $$

My Resume

2009-09-08T00:34:00.010-04:00

I finally had the time to update and upload my resume. I will try to make this a permanent link on the page.

Dr. Orhan Karsligil
orhan at karsligil.com

Education	MASSACHUSETTS INSTITUTE OF TECHNOLOGY Cambridge, MA Laboratory of Intelligent Systems in Process Engineering Ph.D. degree in Chemical Engineering, June 2000. Thesis under Prof. George Stephanopoulos on “Multiscale Modeling, Identification, and Model Predictive Control of Procoptimization algorithms in Quadratic Programming achieving orders of magnitude reduction in complexityessing Systems.” Minor in Nonlinear Mathematics. Applied wavelets to modeling and optimization in order to capture multirate and multiscale features. Created new . Elected member of Sigma Xi and past member of AICHE. Twice elected as president of M.I.T. Turkish Students Association. BOGAZICI UNIVERSITY Istanbul, TURKEY B.S. in Chemical Engineering, June 1995. Graduated with High Honors in seven semesters. Emphasis on process design and economics, control, and optimization. Final project on “Developing a Controllability Index for Heat Exchanger Networks with Bypass Streams.
Experience
11/05-Present 08/09-Present 09/00-Present	MASSACHUSETTS INSTITUTE OF TECHNOLOGY Cambridge, MA Bioinformatics and Metabolic Engineering Laboratory Research Scholar working on network and pattern identification problems, specifically on computational design of Antimicrobial Peptides using motifs extracted from known peptides. THEISS RESEARCH (http://theissresearch.org/) Scientist / Principal Investigator on research projects involving process design and control, signal processing and pattern recognition. THE EXETER GROUP, INC. Cambridge, MA Head of Information Systems, Project Manager Client-facing experience includes leading the development of Online Enrollment Application of a large US University as a Project Manager, managing the upgrade of student management systems for a university in Kuwait as an Assistant Project Manager, designing the security architecture for a B2B project between a prominent bank and an airline company in Kuwait as an Operations Lead, and implementation of Exeter Student Suite for a leading medical school in Boston. Internal project experience includes managing the IT team, managing the upgrade and expansion of the internal IS infrastructure, planning and implementing security policies and audits for the Exeter network, developing strategies and completing the implementation of an Exeter-wide content management system, and developing and implementing Exeter Group’s intranet systems including expense and time tracking, invoicing, reporting, and allocations. MCSE and MCDBA certifications.

Experience





9/00-Present	THE EXETER GROUP, INC. Cambridge, MA Head of Information Systems, Project Manager Client-facing experience includes leading the development of Online Enrollment Application of a large US University as a Project Manager, managing the upgrade of student management systems for a university in Kuwait as an Assistant Project Manager, designing the security architecture for a B2B project between a prominent bank and an airline company in Kuwait as an Operations Lead, and implementation of Exeter Student Suite for a leading medical school in Boston. Internal project experience includes managing the IT team, managing the upgrade and expansion of the internal IS infrastructure, planning and implementing security policies and audits for the Exeter network, developing strategies and completing the implementation of an Exeter-wide content management system, and developing and implementing Exeter Group’s intranet systems including expense and time tracking, invoicing, reporting, and allocations. MCSE and MCDBA certifications.
8/95-6/00	MASSACHUSETTS INSTITUTE OF TECHNOLOGY Cambridge, MA Laboratory for Intelligent Systems in Process Engineering Research Assistant, Teaching Assistant, Seminar Series Organizer, and Systems Administrator.
Summer 1994	PROCTER & GAMBLE, INC. Frankfurt, GERMANY First Line Manager, European Beverages Process Development Department. Project on the solubility of calcium complexes in orange juice concentrate
Publications	“Multi-Scale Modeling, Estimation and Control of Processing Systems”, George Stephanopoulos, Matthew Dyer, and Orhan Karsligil, Computers and Chemical Engineering, 21, p. S797-S803 (1997) “Multi-Scale Considerations in Linear and Nonlinear Estimation and Control”, George Stephanopoulos, Orhan Karsligil and Matthew Dyer, in Nonlinear Model-Based Control, R. Berber and C. Kravaris (editors), Kluwer (1998) “Multi-Scale Model-Predictive Control”, Orhan Karsligil, Matthew Dyer and George Stephanopoulos, Proceedings of DYCOPS-5, Kerkyra, Greece (1998) “Multi-scale Aspects in Model-Predictive Control”, George Stephanopoulos, Orhan Karsligil, and Matthew Dyer, Journal of Process Control, Vol: 10, Issue: 2-3, pp. 275-282 (2000)
Research Interests:	Multiscale Modeling and Optimization in Computational Biology and Protein Folding problems: Using multiscale ideas in modeling and optimization to solve problems in Bioinformatics and Protein Folding. Multiresolution approach to modeling the interactions between sites in a molecule and simplifying the related energy minimization problem. One of the objectives is to convert the big energy minimization problem to an iterative, coarse to fine-scale optimization problem, which can be solved using parallel processors. Another objective is using wavelets or similar signal processing techniques to analyze patterns in gene sequences to identify statistically significant coherent features. Process Design and Control: Application of multiscale modeling and estimation to Model Predictive Control. Application of Multiscale Model Predictive Control to industry problems. The objective is to reduce computational complexity of the MPC so that larger systems can be solved in a feasible timeframe. The multiscale modeling allows incorporation of multirate inputs/outputs and estimation as well. Optimization: Application of Wavelet Theory in discrete optimization problems encountered in control theory. Reduction of complexity of Quadratic Programming problems by transforming underlying state equations into multiresolution/multiscale models and solving the optimization problem with constraints in multiple resolutions. The objective is to develop new algorithms to solve the constrained, thus nonlinear QP problems at different resolutions and reduced complexity. Clustering and Parallel Algorithms: Building a cheap Linux cluster with off-the-shelf components and testing parallel algorithms and database applications which can be used to solve industrial problems as described above.
Teaching Interests	Systems Engineering Numerical Methods in Chemical Engineering Process Design and Control Applicable to Biological Systems Optimization Techniques for Engineering Problems Nonlinear Systems Project Management in IT Networks and Security
Academic Interests	Cross-department/Cross-university Research Organization of seminar series Advanced computer systems to solve large scale problems Commercialization of research results to get industrial funding
Awards	PAD scholarship from German Government 1984 3rd place in Turkish Physics Olympiads, 1986 Valedictorian, Istanbul German High School, 1991 DAAD scholarship from the German Government, 1991 Bogazici Univ. Alumni Association Scholarship, 1991-1995 Bogazici Univ. Professor Turgut Noyan Award, 1995 M.I.T. Chem. Eng. Dept. Graduate Student Fellowship, 1995
Activities	Turkish-American Cultural Society of New England, Inc. Twice elected as Member of the Executive Committee, serving on the Disciplinary Committee
Languages	Fluent in English, German, and Turkish.

TEX test

2009-09-07T00:11:00.003-04:00

Here I am testing a math equation using some JS code:

$$ \pi = \sum_{i=1}^{\infty} i^{2*i} $$

Multidimensional signatures in antimicrobial peptides

2006-01-05T10:54:00.000-05:00

PNAS

Author: Nannette Y. Yount, Michael R. Yeaman

Year: 2005

Category: Bioinformatics Peptides Antimicrobial

Publisher: PNAS

DOI: 10.1073

My short notes

3D motif discovery for antimicrobial peptides: multidimensional signature model. This is a unifying structural theme. Has evolutionary roots, predicts not yet existing peptides and identified known peptides to have antimicrobial properties.

Common peptide properties (i) small proteins (<10kDa), (ii) cationic charges (+2/+7 at pH7), (iii) amphipathic (hydrophobic and hydrophilic facets).

Select a set of peptides from a known set, also include known peptides with yet unknown antimicrobial property but structural similarities.

Prepare a protocal to test the antimicrobial effects (assay for antimicrobial activity).

My ideas

Embedding Antimicrobial Peptides on the surfaces.

Coctail of peptides to check if their interaction with the organisms are based on different processes

Tags: Bioinformatics 3D Motifs Signatures

Structured Blogging

2006-01-05T10:35:00.000-05:00

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

The articles I read and plan to read

2006-01-05T10:09:00.000-05:00

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

Guy Kawasaki's Blog

2006-01-04T15:46:00.000-05:00

Guy Kawasaki

Job: VC (founder), at Garage.com

Blog: “Let the Good Times Roll” by Guy Kawasaki

Profile:

More about history of Guy Kawasaki can be found at his blog:

History and Story of Guy Kawasaki

Deal Finder Search Engine

2006-01-04T11:25:00.000-05:00

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

Noam Slonim's Homepage

2005-12-31T18:23:00.000-05:00

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

2005-12-28T18:30:00.000-05:00

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.

So Wordpress was not able to send emails to users with their account information and it was of course not able to send me emails that there are new users. Now I think the problem is resolved thanks to a very cool plugin: wp-phpmailer

It took me 2 minutes to install and configure it. It works perfectly....

Internet Archive for old Movies (Free)

2005-12-28T12:58:00.000-05:00

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

2005-12-22T12:18:00.000-05:00

Resources and Links for Clustering:

Clustering Software

http://astro.u-strasbg.fr/~fmurtagh/mda-sw/online-sw.html

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

Clustering Review

http://www.elet.polimi.it/upload/matteucc/Clustering/tutorial_html/

Iced cluster

2005-12-22T02:21:00.000-05:00

Iced cluster

Originally uploaded by francom05.

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

Genomic Databases

2005-12-20T13:07:00.000-05:00

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

2005-12-20T11:11:00.000-05:00

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

2005-12-19T12:48:00.000-05:00

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

Finally have pictures on my site

2005-12-19T11:30:00.000-05:00

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

2005-12-16T18:35:00.000-05:00

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

2005-12-14T18:07:00.000-05:00

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

PlanetMath

2005-12-14T17:14:00.000-05:00

Excellent online encyclopedia for anything related to Mathematics.

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

PlanetMath

Global Financial Data

2005-12-14T14:18:00.000-05:00

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

2005-12-13T16:14:00.000-05:00

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

2005-12-13T16:06:00.000-05:00

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

2005-12-12T18:40:00.000-05:00

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

Dictionary of Algorithms and Data Structures

2005-12-12T10:32:00.000-05:00

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

Sanibel Pictures

2005-12-11T19:10:00.000-05:00

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

2005-12-11T19:04:00.000-05:00

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

2005-12-09T16:43:00.000-05:00

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 @nature.com

Scientists discover how cancer spreads - Cancer - MSNBC.com

2005-12-07T20:24:00.000-05:00

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 - MSNBC.com

Helices

2005-12-07T19:37:00.000-05:00

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

2005-12-07T12:10:00.000-05:00

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.

Pelicans sitting in the front yard

2005-12-06T10:28:00.000-05:00

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

2005-12-05T11:21:00.000-05:00

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

2005-12-01T12:14:00.000-05:00

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

2005-11-30T01:16:00.000-05:00

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

Tutorial Links

2005-11-29T19:17:00.000-05:00

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

Least Square Analysis by dropping data points

2005-11-29T02:11:00.000-05:00

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

2005-11-29T01:51:00.000-05:00

Plans for the site

2005-11-25T13:19:00.000-05:00

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

2005-10-03T16:15:00.000-04:00

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: www.writely.com

Orhan out.

Multi-User Desktop - Userful

2005-08-09T22:49:00.000-04:00

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

2005-07-21T15:51:00.000-04:00

Windows Server Hacks: Remotely Enable Remote Desktop

Concurrent Remote Desktop Sessions in Windows XP SP2

New Idea

2005-07-19T11:03:00.000-04:00

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:

2005-07-19T09:23:00.000-04:00

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

2005-07-09T19:13:00.000-04:00

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

2005-07-09T18:59:00.000-04:00

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.

Where was I

2004-11-30T19:30:00.000-05:00

Well I am in Oklahoma....on a project :) Finally managed to fix the pictures. There was a problem with the webserver configurations. Updates killed the server configuration. Fixed now though. Will try to post something substantial this week. Especially on my MultiScale data thresholding research. I have a working code, just need to make some changes to get nicer results.

Fun With Prime Numbers

2004-11-09T23:15:00.000-05:00

Fun With Prime Numbers

Many interesting algorithms to calculate prime numbers. Very exciiting....

Updates

2004-11-03T20:09:00.000-05:00

I added some more articles and information to Technology and Mathematics
categories. My research on Multiscale Data Thresholding is coming along.
I will start putting some intermediate results soon.

Some info I find interesting

2004-11-03T10:14:00.000-05:00

I like simple, basic mathematics. I like theories which can be explained with simple tools. I believe that good ideas should be able to be presented in simple ways. If something can only be described in such a way that a few experts can understand it then it means there is still some work needed in that area to convert it to a simpler form. I am planning to talk about things like Prime Numbers, Encryption, Number Theory, Linear Algebra and Differential Equations and methods to solve these problems using numerical techniques. I hope some of these will turn into lecture notes at some point.

Some of the interesting books I read or am reading currently on math and engineering:

The Code Book by Simon Singh If you are interested in the history of encryption and codes this is a great book. Many interesting ideas about how to attack certain type of combinatorial problems without killing yourself with raw complexity.

Prime Obsession The story of Prime Numbers and the famous Riemann Hypothesis (Short description by Wolfram Research) There is also a proof which is not validated yet (Proof of Riemann Hypothesis)

Initial Link Collection

2004-11-03T10:12:00.000-05:00

I am mostly interested in Process Control, Model Predictive Control, Adaptive Control and Nonlinear Control. I am planning to put here classic links and basic theory. Some Matlab files and relevant book infos.

Some links:

Statistical Process Control from NASA

What is PID (simple and short)?

Other Interesting Tuning Algorithms

Interactive online education site from McMaster

More on PID

Mathematical Methods in Stock Analysis

2004-11-03T09:49:00.000-05:00

This is a collection of articles on various mathematical methods used in stock analysis:

A good starting point for the terms: Evaluation Stocks http://stocks.about.com/od/evaluatingstocks/
Collection of introductory articles on Stock Picking http://www.investopedia.com/university/stockpicking/
Golden ratio and Fibonacci Numbers in Stock Market http://goldennumber.net/stocks.htm
Data Mining Techniques: How to extract useful information from big amount of data: MIT Course on Datamining

This list is going to grow as I find more information. Please add more using the comments.

Chaos and Control

2004-11-01T15:03:00.000-05:00

Chaos, control and controlling chaos are all very interesting topics. This article in NewScientist gives a great example of the use if chaos in control. They designed a robot to be controlled by chaotic functions. It is just a simulation but I believe it is a great start. There is a big gap between computer scientist who develop the algorithms and the people who apply them on real robots or systems. Genetic Algorithms sound very nice on paper, so does simulated annealing, but who wants to wait 5 hours before a single step is calculated. A great read...

Technology Review: Bridging the Genomic Divide

2004-10-19T21:22:00.000-04:00

Very interesting article on combinatorial Chemistry and drug discovery methods.

Technology Review: Bridging the Genomic Divide

That small molecules have more chance to interact with proteins and that there are only very small number of them identified is amazing. Production of small molecules is much easier and thus many more of them can be tested in a combinatorial way. The article also mentiones that NIH is planning to make the results available to public and acedemia.

Beam me to Mars, Scotty!

2004-10-15T15:17:00.000-04:00

Interesting technology...Magnetic Propulsion

I remember that in high school I was thinking about using Bogazici channel (connects Black Sea to Marmara Sea, so it is salty water) and the earths magnetic field to generate electricity. If you calculate between the coasts of the channel there is a mV range difference in potential. If you have very large metal plates you can generate electricity. THe oposite works too : You pump electricity to those plates and with the help of the magnetic field of earth (perpendicular to earth) you can move the water.

New Category: Technology

2004-10-14T11:53:00.000-04:00

I added a new category on Technology. I am going to add links and ideas
about computers, software, technology and science in general to that
category.

Prisoner's Dilemma

2004-10-14T11:50:00.000-04:00

Check this site: Prisoner's Dilemma

It is about the Prisoner's Dilemma competition. The new winner is a set of cooperating agents. Very clever. The rules are so simple but yet the results are so interesting.

First post

2004-10-14T09:48:00.000-04:00

I am planning to use this space to write about computers, software and technology in general.

Switching off gene to stop tumor

2004-10-13T15:50:00.000-04:00

An interesting article on this new finding. Unfortunately gene therapy is still far away from being reality, but it is interesting to play with genes in this way to prevent cancer or similar health issues. The question is though the side effects. How specific can one get in preventing cell division?

Updated the Mathematics Category

2004-10-12T18:41:00.000-04:00

Started working on some new algorithms to test my ideas on event
identification using multiscale thresholding. Check it out at my mathematics category.
.

Data smoothing using multiscale thresh holding

2004-10-12T18:14:00.000-04:00

A signal consists of multiple components occurring at different frequencies. Current analysis methods analyze signals either in time or frequency domain but not in both at the same time. Time series analysis is major topic in signal processing. Any control engineer spends endless nights studying the Fourier transformations which convert a time series into the frequency domain and you can draw fancy graphs and shape your frequency response of your controller. These methods work very nicely for linear systems, meaning if you can open a valve infinitely :).

I am interested in analyzing signals in both domains at the same time. This would enable the use of methodologies from both domains, like constrains and events in time, and data smoothing (multiband frequency filters). Wavelets provide a nice framework for this type of research.

I currently work on simple multiscale threshholding algorithms. The idea and underlying math is extremely simple:

Convert the signal into multiscale domain using Haar wavelets (http://cnx.rice.edu/content/m10764/latest/)
Threshold the difference components (i.e. if less then epsilon set it to zero)
Reconstruct the signal

Next steps are going to be

Use a moving window for the threshholding algorithm to get multiple reconstructed values for the same data points
Analyze these points for variance
Establish an event detection algorithm

I will post some of my results soon.

ScienceWorld - One of the best resources on the web

2004-10-07T14:50:00.000-04:00

ScienceWorld is a very rich scientific treasure box. I recommend everyone to go and take a look.

Multiscale Methods to Speed up QR problems

2004-10-07T14:36:00.000-04:00

My thesis was based on Multiscale Modelling. The building blocks of this methodology are a type of filters called Wavelets. Using wavelets it is possible to transform a first order system to time-frequency domain. In this domain the model representation is not anymore the simple linear time line but a tree structure where both time line (horizontal) and scales (frequency bands - vertical) are represented.

Once the model is transformed into this new domain it is also possible to create algorithms to solve a QR Programming problem based on this first order system. Instead of solving the problem globally it is possible to solve a subset which is a close approximation. This fast solution represents fine resolution at the beginning of the time line and a coarser resolution in the future where uncertainity in most physical systems make finer calculations obsolote anyhow.

I am going to go into more details in the comments section of this post in the next couple days. I will formulate a sample case and demonstrate the solution algorithm. I hope to have some links ready at some point too. Please send comments if you have any.

UPDATE: What is QR? (click here for the source)

The quadratic programming problem involves minimization of a quadratic function subject to linear constraints. Most codes use the formulation

where is symmetric, and the index sets and specify the inequality and equality constraints, respectively.

The difficulty of solving the quadratic programming problem depends largely on the nature of the matrix Q.