An interesting approach to clustering. Minimizing the observers input and emphasizing the information content and correlations of the data.
Noam Slonim's Homepage
Wow it took me some time but I finally solved the email problem. My server does not have an smtp server and because of ISP restrictions it is a nightmare to configure one.
I used to watch black and white SciFi movies when I was a kid... well then everything was black and white since there was no color broadcast until the beginning of 80's in Turkey. I remember the old movies with simple rockets and clay monsters. It is really hard to find those movies on TV or DVD anymore. Somebody did a great job and created a free archive of all those old movies. The archive is searchable and movies can be downloaded. I definetely plan to watch some of the old SciFi movies. Here is the link...
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
http://www.elet.polimi.it/upload/matteucc/Clustering/tutorial_html/
I was searching for clusters ended up with a seasonal picture.. :) Will continue searching tomorrow...
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)
Synthetic Antimicrobial Peptide Database
Antimicrobial Peptide Database from University of Nebraska Medical Center
Antimicrobial Sequences ANTIMIC
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
OpenCourseWare Finder
I managed to get the photos show up on the site. Click on the Photos tab on the navigation bar to go to the picture album. I will continue adding more picture as time allows.
I sometimes forget that our cats were this small when we first got them. Now they are 19lb each...
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
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.
PlanetMath
It outputs HTML/TEX/or JPEG so that the data and equations are reusable.
PlanetMath
Financial Data from different countries for different commodities. Very useful if you need historical data.
Global Financial Data
Global Financial Data
Interesting Articles and tools on Protein Networks and Network Motifs. Need to check the tools.
Uri Alon's Molecular Cell Biology Lab
Uri Alon's Molecular Cell Biology Lab
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
Gene expressionWhich mean do you mean? : Nature Reviews Genetics
A collection of Data Compression algorithms with nice demonstrations. Data-Compression.com
Pretty interesting site with many algorithms and their definitions. Check it out:
Dictionary of Algorithms and Data Structures
Dictionary of Algorithms and Data Structures
Stiched the pictures I took from the balcony manually. Still need to learn how to take this pictures so that automatic stiching works nicer.
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
Patent 6,887,847
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:
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
Scientists discover how cancer spreads - Cancer - MSNBC.com
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.
I am planning to change this post regularly to capture links. I might
add them to the comments and then incorporate them into categories in
the post. The categories might change and I might need to incorporate a
different format at some point, but for now it should be enough. Please
add usefull sites into the comments and please add some detail what
that link is for.
| Category | Link | Description |
| Search | Google | General search engine |
| Google Scholar | Search for papers | |
| Citeseer | Search for papers and citations | |
| ArXiv | Search for papers | |
| Preview Seek | General search with categories | |
| Bioinformatics | Protein Structures | A tutorial on protein structures |
| Antimic. Peptide DB | Antimicrobial Peptide database with additional resources on design. | |
Research
- Post to CiteULike
- ThinkFree Office Online
- Writely - The Web Word Processor
- CiteULike: okarsligil's library
Weird Science
- Global Consciousness Project -- consciousness, group consciousness, mind
- On-Line Encyclopedia of Integer Sequences (Look...
- Deniz Yuret's Math Problems
References
- The Math Forum - Ask Dr. Math
- Institute for Systems Biology: Home
- San Diego Supercomputer Center: Delivering Cyberinfrastructure
- MIT OpenCourseWare | OCW Home
- eFunda: The Ultimate Online Reference for Engineers
- Free Programming and Computer Science Books
- Textbook Revolution
- Welcome
- Dictionary of Algorithms
Software-Tools
- FileForum | TeXnicCenter
- Free Source Code Version Control Software (Revision Control Software) (thefreecountry.com)
- Cytoscape: Analyzing and Visualizing Biological Network Data
- The BUGS Project - Bayesian inference Using Gibbs Sampling
- EndNote - Introductory Tutorial for EndNote7
- Xd3d home page
- The Knowledgebase and Analytical Tools of Bioinformatics
- Bioinformatics.Org: Molecular Linux
- bioknoppix portal - Welcome to bioknoppix home
- DNALinux
- Bio-Linux
Paper Search
- Computer and Information Science Papers CiteSeer Publications ResearchIndex
- arXiv.org e-Print archive
- Google Scholar
- Computer and Information Science Papers CiteSeer Publications ResearchIndex
Online Articles
- ACM
Queue - Hitchhiker's Guide to Biomorphic Software - Discover how
nature's most successful systems can work to inspire your software.
- Bioinformatics Factsheet
- To read during Protein Structure (Block 4).
- Bioinformatics Introduction
- How to Think Like a Computer Scientist: Learning with Python
Online Courses
- MIT
OpenCourseWare | Electrical Engineering and Computer Science | 6.092
Bioinformatics and Proteomics, January (IAP) 2005 | Home
- MIT OpenCourseWare | Sloan School of Management | 15.062 Data Mining, Spring 2003 | Lecture Notes
- MIT OpenCourseWare | Biology | 7.012 Introduction to Biology, Fall 2004 | Video Lectures
- MIT OpenCourseWare | Mathematics | 18.417 Introduction to Computational Molecular Biology, Fall 2004 | Home
- MIT OpenCourseWare | Biology | 7.91J Foundations of Computational and Systems Biology, Spring 2004 | Home
- Game Theory .net - Resources for Learning and Teaching Strategy for Business and Life
- The Biology Project
- Serafim Batzoglou's Website
- cause, chance and Bayesian statistics - Bayes theory for conditional and marginal probabilities
- Bayes Statistics [ISyE 8843] Home Page
- Greg Butler: Bioinformatics Algorithms Course
be very happy today but there are still some of these birds sitting in
the front yard :)
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.
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.
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