tag:blogger.com,1999:blog-5171826918819428882023-11-16T11:04:52.895-05:00Blogwerhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.comBlogger86125tag:blogger.com,1999:blog-517182691881942888.post-20363983709276055752010-09-08T12:20:00.001-04:002010-09-08T12:20:57.603-04:00Long time no post :)I will be moving my research blogging into a private blogging platform hosted on my internal network, but I will continue posting here my daily rants. I am hoping to do it more often. It is definitely relaxing :)werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-77931822388402686622009-11-17T17:31:00.000-05:002009-11-17T17:31:04.828-05:00Ideas around a Motif Cleanup AlgorithmI was trying to create an algorithm that would take the list of motifs/regular expressions and extract redundant sections out of them.<br />
<br />
I think it is easier to explain this with an example:<br />
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<a name='more'></a><br />
<br />
The regular expressions I am dealing with are of the form:<br />
<br />
1. [A B C] [B D] [A C E] [B D E]<br />
2. [A C] [B C] [C E] [B D F]<br />
3. [A B E] [D] [A C D E] [B C E]<br />
<br />
Although these motifs are different from each other if one tries to enumerate all possible instances there are overlapping instances e.g.<br />
1 can create ABDB so does 2.<br />
<br />
One way to clean the motifs so that they do not overlap at all is to take out intersections of motifs in an algorithm like this:<br />
<br />
1. Start from first motif.<br />
2. Find the intersection of the first and second motifs and add the difference between this and the second motif to the list.<br />
3. Add the third motif to the list by adding the difference of 1 and 3's intersection from 3 and then the difference of this newly added element from the intersection of the second element and the newly created third element. So we will have now four elements in our list.<br />
<br />
This sounded good at the beginning until I realized that in this fashion I would need $$2^{n-1}$$ elements for and original n number of motifs and it is not feasible. So I need to think about something else.werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-56568319119982350672009-10-20T16:03:00.002-04:002009-10-20T16:03:47.222-04:00Planning to upgrade my Phone<span style="font-family: arial, sans-serif; font-size: small;"></span><br />
<div style="font-weight: bold;">Android Phones That I am interested in...<br />
</div>I am planning to change my phone/provider after November.<br />
<br />
<a name='more'></a><br />
<br />
I need Exchange connection, GPS, GSM, fast processor and larger than 3.5 inch screen. A keyboard would be nice. iPhones do not need to apply :)<br />
<br />
Any recommendations?<br />
<br />
<br />
<br />
<span style="font-weight: bold;">Motorola Droid</span><br />
3.7 inch screen 480x854 resolution, builtin QWERTY keyboard, OMAP3430 Processor with OpenGL support, Android 2.0 on Verizon assumed to be around $250<br />
<br />
<div style="display: inline; font-family: arial, sans-serif; font-size: small; white-space: normal;"></div><div class="OH" contenteditable="false" style="display: inline-table; font-family: arial, sans-serif; font-size: small; margin-bottom: 0px; margin-left: 2px; margin-right: 0px; margin-top: 5px; position: relative; white-space: normal;"><w:caption style="-webkit-user-modify: read-only; background-color: white; color: black; display: block; outline-color: initial; outline-style: initial; outline-width: 0px; padding-bottom: 4px; padding-left: 4px; padding-right: 4px; padding-top: 4px; text-align: center; white-space: pre-wrap;">Motorola Droid</w:caption><br />
</div><br />
<span style="font-weight: bold;">Acer A1 Liquid</span><br />
3.8inch screen, 800x400 resolution 1GHz SnapDragon 8250 Android 1.6<br />
<br />
<div class="OH" contenteditable="false" style="display: inline-table; font-family: arial, sans-serif; font-size: small; margin-bottom: 0px; margin-left: 2px; margin-right: 0px; margin-top: 5px; position: relative; white-space: normal;"><w:caption style="-webkit-user-modify: read-only; background-color: white; color: black; display: block; outline-color: initial; outline-style: initial; outline-width: 0px; padding-bottom: 4px; padding-left: 4px; padding-right: 4px; padding-top: 4px; text-align: center; white-space: pre-wrap;">Acer-A1-Android-Phone</w:caption><br />
</div><br />
<span style="font-weight: bold;">A</span><span style="font-weight: bold;">rchos Tablet Phone</span><br />
4.3 inch, 854x480<br />
<br />
<div class="OH" contenteditable="false" style="display: inline-table; font-family: arial, sans-serif; font-size: small; margin-bottom: 0px; margin-left: 2px; margin-right: 0px; margin-top: 5px; position: relative; white-space: normal;"><w:caption style="-webkit-user-modify: read-only; background-color: white; color: black; display: block; outline-color: initial; outline-style: initial; outline-width: 0px; padding-bottom: 4px; padding-left: 4px; padding-right: 4px; padding-top: 4px; text-align: center; white-space: pre-wrap;">archos_phone_tablet_slashgear_1-540x323</w:caption><br />
</div><br />
<span style="font-weight: bold;">Sony Ericsson Xperia X3</span><br />
4 inch, SnapDragon Processor<br />
<br />
<div class="OH" contenteditable="false" style="display: inline-table; font-family: arial, sans-serif; font-size: small; margin-bottom: 0px; margin-left: 2px; margin-right: 0px; margin-top: 5px; position: relative; white-space: normal;"><w:caption style="-webkit-user-modify: read-only; background-color: white; color: black; display: block; outline-color: initial; outline-style: initial; outline-width: 0px; padding-bottom: 4px; padding-left: 4px; padding-right: 4px; padding-top: 4px; text-align: center; white-space: pre-wrap;">sony-ericsson-x3-xperia</w:caption><br />
</div>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-60453839491834533242009-10-19T14:33:00.000-04:002009-10-19T14:33:56.851-04:00Horrible DriversEverybody has bad days in traffic. Lately I started having more than one bad day a week. Just today in the morning I was getting killed by an idiot who was either texting or searching for something, or putting a CD into the CD player or eating/drinking something while drinking. He was driving right in front of me. I saw the guys head disappearing a couple times and he moved between the lanes while doing that. Lucky him there was no one in the other lane. Then again he was doing something other than driving and suddenly the traffic slowed but since he was not looking he had to react drastically when he again had a chance to look in front of him. He hit the breaks, the tires locked and he swirled like crazy, turning almost 90 degrees and then miraculously was able to gain control... he was almost hitting me since I was unlucky at that moment being in the next lane.<br />
<br />
This happening more and more. Phone in one hand coffee in the other.. who or what is holding the driving wheel? Worst is the people turning and talking on the phone. They cannot signal since they hold the phone with their left hand, the right being their driving wheel hand, then they cannot turn quickly since can only use one hand and to top it off they do not pay attention to the traffic since they are doing too many things at the same time. If you honk they get angry and start telling their friend on the phone about this rude guy having a road rage...well some of us want to go home in one piece. People who want to talk on the phone while driving should be in one lane... let them kill each other. I think it is time to require hand free sets for every new car. Even that is bad but at least people can use half of their brains and both of their hands.werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-49272761385648161792009-10-01T09:39:00.004-04:002009-10-05T09:45:55.303-04:00Feasibility of BioFuelsOkay everybody is talking about Biofuels. All big companies are investing in biofuels. Some do it to look nice and use it as a PR stunt (most oil companies), knowing that the current attempts will not even make a dent in their market share or profits, some others do it because it might be profitable in the short term locally, but globally I need to see proof of its feasibility.<br />
<br />
<a name='more'></a><br />
First of all you need to build either hundreds of large (very very large) plants to process the biowastes, or crops. You need to transfer them in (constantly), you need to store them, process them, ferment them in huuuggeee tanks, then filter them, purify them, get rid of the waste and transfer the product to the market. You will need to control these plants very gently, since you will be using organisms you need to make sure temperatures do not swing much (it gets cold in midwest where the crops are easy to get), you have to maintain and mix carefully to keep things going (either huge tanks or huge number of tanks…). Or you can build thousands of smaller plants that can handle local crops. Then capital costs will skyrocket. Even if you can streamline the plants by standardizing on parts, can you imaging recalling 200,000 biofuel plants because of faulty valves? Also grass grows for half of the year, what are they going to use for the rest of the year? At some point you will need to tap into the food stock. It will increase the food costs, which in affect will have a worse effect on low income population then high fuel costs. You can do without driving but you cannot do without eating. As I said somebody has to show me in clear math how this would work.<br />
<br />
I would be more interested using garbage and landfills as organic source for biofuels. It is produced constantly. There is an abundance of it. Nobody needs it, everybody is trying to get rid of it. You can use that and the CO2 from the air to convert it to biofuels… Less garbage, less CO2, less dangerous wastes and you also get biofuels. I even have the name for the company: GARBAGAS!<br />
<br />
Update: Apparently there is already a company doing this. Not using biotech but old style chemical engineering techniques:<br />
<br />
<br />
<object height="344" width="425"><param name="movie" value="http://www.youtube.com/v/twQA4cUwYus&hl=en&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/twQA4cUwYus&hl=en&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object><br />
<br />
<br />
Update 2: Okay there is more news on this topic. More people are looking into alternative sources for biofuels. Instead of using/abusing corn more research is done on creating gasoline directly from other types of wastes. Check newhere and here.<br />
<br />
I think in the next 18 months there will be a very big change of direction in Biofuel research. Especially change in administration might change policy. I also expect big oil companies getting little more nervous about the new high throughput alternatives.werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-30746316795000346742009-09-29T16:18:00.001-04:002009-09-29T16:19:28.263-04:00September 2009 AMP Design UpdateI updated the design algorithm over the last couple of months to be more rigorous and to incorporate underlying data and experimental result biases. Below you can find the presentation.<br />
<br />
<a name='more'></a><br />
<br />
<div><br />
</div><div><iframe frameborder="0" height="342" src="http://docs.google.com/present/embed?id=at3jqgchkxr_56c6m89tcp" width="410"></iframe><br />
</div>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com1tag:blogger.com,1999:blog-517182691881942888.post-37463760689359246882009-09-24T17:48:00.005-04:002009-09-27T11:21:07.771-04:00Musings with VolatilityVolatility is a vague term. There are strict definitions but within limited context. There is always something "implied".<br />
<br />
I will try to do some research and find some answers for my questions.<br />
<a name='more'></a><span style="font-size: x-large;">Definitions:</span><br />
<br />
<br />
<a href="http://en.wikipedia.org/wiki/Volatility_(finance)">Financial Volatility:</a><br />
<blockquote>Volatility most frequently refers to the standard deviation of the continuously compounded returns of a financial instrument with a specific time horizon. It is often used to quantify the risk of the instrument over that time period. Volatility is typically expressed in annualized terms, and it may either be an absolute number ($5) or a fraction of the mean (5%). <i>from Wikipedia</i><br />
</blockquote><a href="http://en.wikipedia.org/wiki/Stochastic_volatility"><i>Stochastic Volatility</i></a><i>: </i><br />
<blockquote>The name derives from the models' treatment of the underlying security's volatility as a <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Random_process" style="background-attachment: initial; background-clip: initial; background-image: none; background-origin: initial;" title="Random process"><span style="color: black;">random process</span></a>, governed by <a href="http://en.wikipedia.org/wiki/State_variable" style="background-attachment: initial; background-clip: initial; background-image: none; background-origin: initial;" title="State variable"><span style="color: black;">state variables</span></a> such as the price level of the underlying, the tendency of volatility to revert to some long-run mean value, and the <a href="http://en.wikipedia.org/wiki/Variance" style="background-attachment: initial; background-clip: initial; background-image: none; background-origin: initial;" title="Variance"><span style="color: black;">variance</span></a> of the volatility process itself, among others. <i>from Wikipedia</i><br />
</blockquote><br />
<br />
<span style="font-size: x-large;">My Take</span><br />
<br />
Now there is so much about volatility that depends on the context that it is hard to talk about the same thing in different areas of interest (finance, process control, signal processing etc).<br />
<br />
Since I will be introducing my bias, too, at least I should define some of the concepts that I base my view.<br />
<img alt="<<Fig: S&P 500 daily close-to-close returns>>" src="http://staff.science.uva.nl/~marvisse/volatility/close_to_close_returns_sp500.png" /><br />
Assume there is a timeseries data T (like stock data as above). Then the consensus is to convert it to a daily percentage change format:<br />
<div style="text-align: center;">$$ P_{i}=\frac{T_{i}-T_{i-1}}{T_{i}}$$<br />
</div><div style="text-align: left;">Then the day to day percentage changes can be treated as components of the volatility. People then describe the above diagram with phrases like volatility clustering. Day to day changes are interesting (or one can also find day to day ratios which would fluctuate around 1) but it assumes that the expected percentage change is zero, which is not the case, actually the expectation is that it is not zero and that is why people invest (both short and long).<br />
<br />
In my mind the definition of volatility is variability around a modelled behavior. It is basically an indication of the accuracy of the underlying model. If the model is good then the volatility should be low and uniform. If the model is bad then a fluctuating volatility should be expected. So for me:<br />
$$ \Delta_{i}=M_{i}-T_{i}$$<br />
$$ \mu=\frac{1}{n}\sum_{k=1}^n{\Delta_{k}}$$<br />
$$ \sigma^2=\frac{1}{n-1}\sum_{k=1}^n{(\Delta_{k}-\mu)^2}$$<br />
</div>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-40390623499476124232009-09-24T15:07:00.012-04:002009-10-06T18:07:46.565-04:00Online Books and ResourcesMy objective with this thread is adding links to online resources that might be relevant to my research. This should be a linked page from the home page.<br />
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<a name='more'></a><br />
<br />
<span style="font-size: x-large;">Online Paper Collection</span><br />
<br />
<br />
<ul><li><a href="http://www.citeulike.org/user/okarsligil#">CiteULike Library</a> with my paper collections</li>
</ul><br />
<span style="font-size: x-large;"><br />
</span><br />
<span style="font-size: x-large;">Online Courses</span><br />
<div class="separator" style="clear: both; text-align: center;"><a href="http://oyc.yale.edu/yale/portal_skins/custom/images/polak_home_poster.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"></a><br />
</div><a href="http://oyc.yale.edu/yale/portal_skins/custom/images/polak_home_poster.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"></a><br />
<blockquote><a href="http://oyc.yale.edu/yale/portal_skins/custom/images/polak_home_poster.jpg" imageanchor="1" style="clear: left; display: inline !important; margin-bottom: 1em; margin-right: 1em;"><img alt="course images" border="0" height="68" src="http://oyc.yale.edu/yale/portal_skins/custom/images/polak_home_poster.jpg" style="cursor: move;" width="200" /></a><span style="-webkit-text-decorations-in-effect: none; color: black;"><a href="http://oyc.yale.edu/economics/game-theory"><span style="color: black;">Game Theory with Professor Ben Polak</span></a></span><br />
</blockquote><br />
<div class="" style="clear: both; text-align: center;"><br />
</div><div style="text-align: left;"><br />
</div><br />
<span style="font-size: x-large;">Online Books</span><br />
<ul><div class="separator" style="clear: both; text-align: center;"><a href="http://www.gaussianprocess.org/gpml/rwcover.gif" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"></a>
</div><a href="http://www.gaussianprocess.org/gpml/rwcover.gif" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"></a>
</ul><blockquote><a href="http://www.gaussianprocess.org/gpml/rwcover.gif" imageanchor="1" style="clear: left; display: inline !important; margin-bottom: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="96" src="http://www.gaussianprocess.org/gpml/rwcover.gif" style="cursor: move;" width="77" /></span></a><a href="http://www.gaussianprocess.org/gpml/"><span style="color: black;">Gaussian Processes</span></a> <a href="http://www.gaussianprocess.org/gpml/"><span style="color: black;">for Machine</span></a> <a href="http://www.gaussianprocess.org/gpml/"><span style="color: black;">Learning</span></a><br />
</blockquote><blockquote><img alt="Book cover" height="96" src="http://www.inf.fu-berlin.de/~rojas/neural/umschlag.gif" style="cursor: move;" width="63" /> <a href="http://page.mi.fu-berlin.de/rojas/neural/"><span style="color: black;">Neural Networks - A Systematic Introduction</span></a><br />
</blockquote><blockquote><img height="75" src="http://www.cs.cornell.edu/home/kleinber/networks-book/adamic-hier.jpg" style="cursor: move;" width="96" /> <span style="color: black;"><a href="http://www.cs.cornell.edu/home/kleinber/networks-book/">Networks, Crowds, and Markets</a> </span><br />
</blockquote><blockquote><span style="color: black;"><img alt="See inside" height="57" src="http://meboo.convexoptimization.com/images/CoverProductionOLD.jpg" style="cursor: move;" width="96" /> <a href="http://meboo.convexoptimization.com/Meboo.html"><span style="color: black;">Convex Optimization & Euclidean Distance Geometry</span></a></span><br />
</blockquote><blockquote><img alt="[Dive Into Python]" height="96" src="http://www.diveintopython.org/images/cover-small.jpg" width="72" /> <a href="http://www.diveintopython.org/toc/index.html"><span style="color: black;">Dive into Python</span></a><br />
</blockquote><br />
<a href="http://www.diveintopython.org/toc/index.html"></a><br />
<a href="http://meboo.convexoptimization.com/Meboo.html"></a><br />
<a href="http://page.mi.fu-berlin.de/rojas/neural/"></a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-1646434249431736632009-09-22T12:20:00.000-04:002009-09-24T00:22:20.867-04:00Email Posting Of Blog EntriesToday 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.<br /><a name='more'></a><br />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 :).<br /><br />Orhan out,werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-38456919246700223832009-09-15T14:44:00.000-04:002009-09-24T00:22:20.867-04:00Asked at LunchToday when I was eating my Sashimi at <a href="http://www.shogunwestnewton.com/" target="_blank">Shogun</a> one of the regulars who I talk to about history and Turkish language asked me about a Turkish movie he watched recently (<a href="http://www.imdb.com/title/tt0388189/" target="_blank">Kurtulus Savasi</a>).<br /><a name='more'></a>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…werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-79326987871835697682009-09-15T14:13:00.000-04:002009-09-24T00:22:20.867-04:00Ideas about my BlogI am planning to create some workflow around my blog posting process. I am planning to make some entries<br /><a name='more'></a> “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.werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-61344387913989649042009-09-15T14:08:00.000-04:002009-09-24T00:22:20.868-04:00Finally blog migratedAfter 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:<br /><ol><li>Exported content from all my other Blogspot blogs and imported them into my main blog.</li><li>Exported my Wordpress blog content than converted the xml file into blogger import format and imported that into my main blog.</li><li>Searched and found a new template.</li><li>Customized the new template, added some gadgets.</li><li>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: $$ \pi=\sqrt{sample} $$</li></ol>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-41237323952401484982009-09-07T00:11:00.000-04:002009-09-24T00:22:20.868-04:00TEX testHere I am testing a math equation using some JS code:<br /><br />$$ \pi = \sum_{i=1}^{\infty} i^{2*i} $$werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-88452599954142363782006-01-05T10:54:00.000-05:002009-09-24T00:22:20.868-04:00Multidimensional signatures in antimicrobial peptides<div class='hreview x-wpsb-review-article'> <div> <h3 class='item fn'><a class='url' href='http://www.pnas.org/cgi/doi/10.1073/pnas.0401567101'>PNAS</a></h3> <p><b>Author</b>: Nannette Y. Yount, Michael R. Yeaman</p> <p><b>Year</b>: 2005</p> <p><b>Category</b>: Bioinformatics Peptides Antimicrobial</p> <p><b>Publisher</b>: PNAS</p> <p><b>DOI</b>: 10.1073</p> </div> <div class='description'><p><h3>My short notes</h3><br/>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.<br/><br/>Common peptide properties (i) small proteins (<10kDa), (ii) cationic charges (+2/+7 at pH7), (iii) amphipathic (hydrophobic and hydrophilic facets).<br/><br/>Select a set of peptides from a known set, also include known peptides with yet unknown antimicrobial property but structural similarities.<br/><br/>Prepare a protocal to test the antimicrobial effects (assay for antimicrobial activity).<br/><br/><p></p><br/><h3>My ideas</h3><br/><ul><br/><li>Embedding Antimicrobial Peptides on the surfaces. </li><br/><li>Coctail of peptides to check if their interaction with the organisms are based on different processes</li><br/><li></li></p></div> <p><b>Tags</b>: Bioinformatics 3D Motifs Signatures</p> </div><br/><script type="application/x-subnode; charset=utf-8"><br/> <!-- the following is structured blog data for machine readers. --><br/> <subnode xmlns:data-view="http://www.w3.org/2003/g/data-view#" data-view:interpreter="http://structuredblogging.org/subnode-to-rdf-interpreter.xsl" xmlns="http://www.structuredblogging.org/xmlns#subnode"><br/> <xml-structured-blog-entry xmlns="http://www.structuredblogging.org/xmlns"><br/> <generator id="wpsb-1" type="x-wpsb-post" version="1"/><review type="review/article"><subject name="PNAS" author="Nannette Y. Yount, Michael R. Yeaman" year="2005" category="Bioinformatics Peptides Antimicrobial" publisher="PNAS" url="http://www.pnas.org/cgi/doi/10.1073/pnas.0401567101" isbn="10.1073"/><rating max="5" min="0"/><description><h3>My short notes</h3><br/>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.<br/><br><br/>Common peptide properties (i) small proteins (<10kDa), (ii) cationic charges (+2/+7 at pH7), (iii) amphipathic (hydrophobic and hydrophilic facets).<br/><br><br/>Select a set of peptides from a known set, also include known peptides with yet unknown antimicrobial property but structural similarities.<br/><br><br/>Prepare a protocal to test the antimicrobial effects (assay for antimicrobial activity).<br/><br><br/><p></p><br/><h3>My ideas</h3><br/><ul><br/><li>Embedding Antimicrobial Peptides on the surfaces. </li><br/><li>Coctail of peptides to check if their interaction with the organisms are based on different processes</li><br/><li></li></description><tags>Bioinformatics 3D Motifs Signatures</tags></review><br/> </xml-structured-blog-entry><br/> </subnode><br/> </script>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-84002679519852036482006-01-05T10:35:00.000-05:002009-09-24T00:22:20.868-04:00Structured BloggingWhen 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.<br />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.<br />Finally 2 days ago I found something that might work: <a href="http://structuredblogging.org/">Structured Blogging</a> 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.<br />I will try to use it as much as possible in the future. I will post an update how things go.<br /><br /><br />Technorati Tags: <a rel="tag" href="http://technorati.com/tag/StructuredBlogging">StructuredBlogging</a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-30687057747388034422006-01-05T10:09:00.000-05:002009-09-24T00:22:20.869-04:00The articles I read and plan to readI 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.<br /><br />You can reach my library from this link: <a href="http://www.citeulike.org/user/okarsligil">Orhan's library</a><a href="http://technorati.com/tag/PapersResearchCitation" rel="tag"></a><br /><a href="http://technorati.com/tag/Citation" rel="tag"></a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-49991289449664977442006-01-04T15:46:00.000-05:002009-09-24T00:22:20.869-04:00Guy Kawasaki's Blog<div class='vcard'> <h3 class='fn'><span class='given-name'>Guy</span> <span class='family-name'>Kawasaki</span></h3> <p><b>Job</b>: <span class='title'>VC (founder)</span>, at <span class='org'>Garage.com</span></p> <p><b>Blog</b>: <a class='url' href='http://blog.guykawasaki.com/'>“Let the Good Times Roll” by Guy Kawasaki</a></p> <p><b>Profile</b>: <p>More about history of Guy Kawasaki can be found at his blog:<br/><br/><a href="http://blog.guykawasaki.com/2005/12/to_build_a_case.html"> History and Story of Guy Kawasaki</a></p></p> </div> <br/><script type="application/x-subnode; charset=utf-8"><br/> <!-- the following is structured blog data for machine readers. --><br/> <subnode xmlns:data-view="http://www.w3.org/2003/g/data-view#" data-view:interpreter="http://structuredblogging.org/subnode-to-rdf-interpreter.xsl" xmlns="http://www.structuredblogging.org/xmlns#subnode"><br/> <xml-structured-blog-entry xmlns="http://www.structuredblogging.org/xmlns"><br/> <generator id="wpsb-1" type="x-wpsb-post" version="1"/><showcase firstname="Guy" lastname="Kawasaki" type="showcase/person"><address state="CA" country="USA"/><job employer="Garage.com">VC (founder)</job><blog url="http://blog.guykawasaki.com/">“Let the Good Times Roll” by Guy Kawasaki</blog><description>More about history of Guy Kawasaki can be found at his blog:<br/><br/><a href="http://blog.guykawasaki.com/2005/12/to_build_a_case.html"> History and Story of Guy Kawasaki</a></description></showcase><br/> </xml-structured-blog-entry><br/> </subnode><br/> </script>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-81569746770003927172006-01-04T11:25:00.000-05:002009-09-24T00:22:20.869-04:00Deal Finder Search EngineIf 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.<br/><a href="http://www.clipfire.com/">Find great deals from the best websites on the newest products</a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-35370083752890877702005-12-31T18:23:00.000-05:002009-09-24T00:22:20.870-04:00Noam Slonim's HomepageAn interesting approach to clustering. Minimizing the observers input and emphasizing the information content and correlations of the data.<br/><a href="http://www.princeton.edu/~nslonim/">Noam Slonim's Homepage</a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-88049654845331617702005-12-28T18:30:00.000-05:002009-09-24T00:22:20.870-04:00Finally resolved the email problemWow 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.<a name='more'></a><br/><br/>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: <a target="_blank" href="http://www.coffee2code.com/archives/2004/06/28/plugin-wpphpmailer/">wp-phpmailer</a><br/><br/>It took me 2 minutes to install and configure it. It works perfectly....werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com2tag:blogger.com,1999:blog-517182691881942888.post-3106800383785042732005-12-28T12:58:00.000-05:002009-09-24T00:22:20.870-04:00Internet 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 <a href="http://www.archive.org/details/movies">link...</a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com2tag:blogger.com,1999:blog-517182691881942888.post-62012175598615632712005-12-22T12:18:00.000-05:002009-09-24T00:22:20.870-04:00Clustering Techniques and Software<h2>Resources and Links for Clustering:</h2><br/><h3>Clustering Software</h3><br/><ul><li><a href="http://astro.u-strasbg.fr/%7Efmurtagh/mda-sw/online-sw.html"><span>http://astro.u-strasbg.fr/~fmurtagh/mda-sw/online-sw.html</span></a></li></ul><ul><li><a href="http://www-users.cs.umn.edu/~karypis/cluto/index.html">gCluto</a> : I started testing it. It has a simple but nice data management tool set, clustering selector and a graph viewer.<br /></li></ul><p> </p><br/><h3>Clustering Review</h3><br/><a href="http://www.elet.polimi.it/upload/matteucc/Clustering/tutorial_html/"><span>http://www.elet.polimi.it/upload/matteucc/Clustering/tutorial_html/</span></a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-24557300917268056602005-12-22T02:21:00.000-05:002009-09-24T00:22:20.871-04:00Iced cluster<div style="float: right; margin-left: 10px; margin-bottom: 10px;"><br/> <a title="photo sharing" href="http://www.flickr.com/photos/93256493@N00/65196186/"><img style="border: 2px solid rgb(0, 0, 0);" src="http://static.flickr.com/34/65196186_dce0fb5d61_m.jpg" /></a><br/> <br/> <span style="font-size: 0.9em; margin-top: 0px;"><br/> <a href="http://www.flickr.com/photos/93256493@N00/65196186/">Iced cluster</a><br/> <br/> Originally uploaded by <a href="http://www.flickr.com/people/93256493@N00/">francom05</a>.<br/> </span><br/></div><br/>I was searching for clusters ended up with a seasonal picture.. :) Will continue searching tomorrow...<br/><br clear="all" />werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-73191414776998976872005-12-20T13:07:00.000-05:002009-09-24T00:22:20.871-04:00Genomic Databases<p> </p><h2> General Resources</h2><a href="http://www3.oup.co.uk/nar/database/c/">Nucleic Acids Research Database Lists contains links to many databases related to genomic data. Excellent resource.</a> <p> </p><h2>Antimicrobial Peptides</h2><p><a href="http://www.bbcm.units.it/%7Etossi/pag2.htm">Antiinfective Peptides Laboratory (Trieste, Italy)</a> </p><p><a href="http://www.cryst.bbk.ac.uk/peptaibol/sequence.htm">Peptaibol Database</a> </p><p><a href="http://oma.terkko.helsinki.fi:8080/%7ESAPD/login">Synthetic Antimicrobial Peptide Database</a></p><p><a href="http://oma.terkko.helsinki.fi:8080/%7ESAPD/login"></a><a href="http://aps.unmc.edu/AP/main.php">Antimicrobial Peptide Database from University of Nebraska Medical Center</a></p><p><a href="http://aps.unmc.edu/AP/main.php"></a><a href="http://www.research.i2r.org.sg/Templar/DB/ANTIMIC/">Antimicrobial Sequences ANTIMIC</a><br /></p><br/><p> </p>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0tag:blogger.com,1999:blog-517182691881942888.post-66977479108540834282005-12-20T11:11:00.000-05:002009-09-24T00:22:20.871-04:00OpenCourseWare FinderUsing 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.<br/><a href="http://opencontent.org/ocwfinder">OpenCourseWare Finder</a>werhttp://www.blogger.com/profile/10582032136711601638noreply@blogger.com0