My 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.
Showing posts with label Resources. Show all posts
Showing posts with label Resources. Show all posts
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
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
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
You can reach my library from this link: Orhan's library
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
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
Find great deals from the best websites on the newest products
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/
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
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
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
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
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.
This is placeholder page for the important tutorial like sites and links for mostly Bioinformatics type sites
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