Downloads | CVS access | CVS Repository | Files | MAEPlugins | Javadocs |
Revision history | Versions Friday, March 31, 2006
MicroArray Explorer Page
MicroArray Explorer Page: " Home | Project Summary | Introduction | Manual | PDFs | Tutorial | Mozilla license | Disclaimer |
Downloads | CVS access | CVS Repository | Files | MAEPlugins | Javadocs | Revision history | Versions "
Downloads | CVS access | CVS Repository | Files | MAEPlugins | Javadocs |
Revision history | Versions 
Gene Expression and Microarrays
Gene Expression and Microarrays: "These are a collection of Gene Expression and Microarrays links."
Welcome to the utPLSQL Project
Welcome to the utPLSQL Project: "Welcome to the utPLSQL Project
This is the utPLSQL Sourceforge site for developers using and developing utPLSQL. The Sourceforge project summary is here.
What is it?
utPLSQL is a unit testing framework for programmers using Oracle's PL/SQL language. Developed by Steven Feuerstein, author of many books on the subject, it allows the automated testing of packages, functions and procedures. For background on the project and the reasons why this sort of unit testing is a good idea, visit the utPLSQL site of the O'Reilly and Associates Oracle Resource Center."
This is the utPLSQL Sourceforge site for developers using and developing utPLSQL. The Sourceforge project summary is here.
What is it?
utPLSQL is a unit testing framework for programmers using Oracle's PL/SQL language. Developed by Steven Feuerstein, author of many books on the subject, it allows the automated testing of packages, functions and procedures. For background on the project and the reasons why this sort of unit testing is a good idea, visit the utPLSQL site of the O'Reilly and Associates Oracle Resource Center."
Qute: Quick Unit Test Engine
Qute: Quick Unit Test Engine: "Qute (Quick Unit Test Engine) is a tool to help you define, generate and run unit tests for the programs you write. Currently, Qute concentrates on support for the testing of Oracle PL/SQL programs."
The following presentations will help you learn how to take advantage of Qute to design, generate and run tests.
You will need to play these webinars from Internet Explorer; you can verify that your browser and computer are compatible for these recordings by clicking here.
Finally, if you are having difficulty getting the recordings to play, hold down the Control key and then click on the "Click here to view" link.
Introduction to Qute
Using Qute to test PL/SQL collections
Using Qute to test cursor variables
Qnxo: Quality In, Excellence Out.
Qnxo: Quality In, Excellence Out.: "Improve productivity and code quality with Qnxo™
PL/SQL developers spend lots of time writing the same kind of code over and over again, much of it based on the underlying tables, views and programs with which we are working. To save time, we frequently take a 'quick and dirty' approach, which is often incomplete and error-prone.
But now, with Qnxo™, you can choose the best-practice path every time while actually increasing your productivity. You can do it all right from within your favorite editor.
And it takes just three steps:
1. Generate a PL/QL code library customized to your database objects.
2. Position Codebar, the always-on-top code toolbar, in your editor.
3. Find what you need in Codebar and copy it instantly into your editor."
PL/SQL developers spend lots of time writing the same kind of code over and over again, much of it based on the underlying tables, views and programs with which we are working. To save time, we frequently take a 'quick and dirty' approach, which is often incomplete and error-prone.
But now, with Qnxo™, you can choose the best-practice path every time while actually increasing your productivity. You can do it all right from within your favorite editor.
And it takes just three steps:
1. Generate a PL/QL code library customized to your database objects.
2. Position Codebar, the always-on-top code toolbar, in your editor.
3. Find what you need in Codebar and copy it instantly into your editor."
Bioinformatics Information
Bioinformatics Information
Courses
List of Bioinformatics Courses at Rockefeller
Bioinformatics
- S-Star.org
- Introduction to Computational Molecular Biology and Genomics (MIT)
- Computational Molecular Biology (Stanford University)
- Representations and Algorithms for Computational Molecular Biology (Stanford University)
- Computational Genomics (Stanford)
- Genomics, Bioinformatics & Medicine (Stanford University)
- Introduction to Computer Programming for Biology (Stanford University)
- Computational Molecular Biology (Washington University in Saint Louis)
- Computational Biology (University of Washington, Seattle)
- Genomics and Computational Biology (Harvard)
- Algorithms for Molecular Biology (Tel Aviv University)
- DNA and Protein Sequence Analysis (Boston University)
- Computational Biology (Carnegie Mellon University)
- VSNS Biocomputing Hypertext Coursebook (University of Bielefeld, Germany)
- Bioinformatics & Computational Genomics Courses (Weismann Institute)
Protein Structure
Genomics
Population Genetics, Molecular Evolution, SNPs
Welcome to Bioconductor
Welcome to Bioconductor
BioC2005 Conference scheduled for August in Seattle
May 19th, 2005 - Bioconductor 1.6 Released
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
Getting started with Bioconductor
To get started with Bioconductor 1.6, you must have R 2.1.x installed.
- You need to have R installed. Instructions on obtaining and installing R.
- Instructions on installing Bioconductor 1.6
Information on using R and Bioconductor
- Bioconductor vignettes
- Bioconductor FAQ
- R documentation
Thursday, March 30, 2006
stu nicholls | CSS PLaY | A CSS Photograph Gallery
TUTORIAL
Creating an Photograph Gallery using CSS only
Introduction
stu nicholls | CSS PLaY | A CSS Photograph Gallery: "One of the many uses for personal and professional web site is to display a gallery of photographs that show off your skills with a camera. Until now these galleries have been produced using javascript, PHP or CGI.
However there is now another way.
With this article I hope to show you how to produce a professional quality photograph gallery using nothing more than an unordered list of photographs and a Cascading Style Sheet (CSS). I will take you through the styling one step at a time and end up converting:"
Creating an Photograph Gallery using CSS only
Introduction
stu nicholls | CSS PLaY | A CSS Photograph Gallery: "One of the many uses for personal and professional web site is to display a gallery of photographs that show off your skills with a camera. Until now these galleries have been produced using javascript, PHP or CGI.
However there is now another way.
With this article I hope to show you how to produce a professional quality photograph gallery using nothing more than an unordered list of photographs and a Cascading Style Sheet (CSS). I will take you through the styling one step at a time and end up converting:"
Freeflux.net - Free CMS & Blog Hosting with Flux CMS
Freeflux.net - Free CMS & Blog Hosting with Flux CMS: "GET YOUR OWN Flux CMS. FOR FREE. GET IT HERE AND NOW.
* It's free *
* It's a CMS, not 'just' a blog
* It's based on Open Source technology (you can even download and use the software by yourself)
* It's continously improving. We (and others) actively develop Flux CMS
If you register now, you will get your free freeflux.net account almost immediatly.
* Paid accounts with no ads and more options are also available, but the free accounts will always be free
Features
See the full feature list for a more complete overview"
* It's free *
* It's a CMS, not 'just' a blog
* It's based on Open Source technology (you can even download and use the software by yourself)
* It's continously improving. We (and others) actively develop Flux CMS
If you register now, you will get your free freeflux.net account almost immediatly.
* Paid accounts with no ads and more options are also available, but the free accounts will always be free
Features
See the full feature list for a more complete overview"
Wednesday, March 29, 2006
ENGENE - DNA array Data Processing and Exploratory Data Analysis
ENGENE - DNA array Data Processing and Exploratory Data Analysis: "engeneTM, a versatile, web-based and platform independent exploratory data analysis tool for gene expression data that aims at storing, visualizing and processing large sets of expression patterns. engene (standing for Gene Engine) integrates a variety of analysis tools for visualizing, pre-processing and clustering expression data. "
Tuesday, March 28, 2006
StatsRUs
StatsRUs: "Rtips"
If you need a tip sheet for R, here it is.
If you need a tip sheet for R, here it is.
This is not a substitute for R documentation, just a list of things I'm using to remember what I read in the email list.
Heed the words of Brian D. Ripley, "One enquiry came to me yesterday which suggested that some users of binary distributions do not know that R comes with two Guides in the doc/manual directory plus an FAQ and the help pages in book form. I hope those are distributed with all the binary distributions (they are not made nor installed by default). Windows-specific versions are available in PDF in rw1001d1.zip and rw1001d2.zip"
Credit for the FaqManager software goes to Stas Bekman, its author.
Intro to R
Intro to R: "Type ls() or objects() to list the objects (data and functions) in your .RData file."
OracleBlog: Bookmark This Page
OracleBlog: Bookmark This Page: "Bookmark This Page"
For Newbies:
Tuesday, December 20, 2005
20 Beginner Oracle Questions
Friday, June 17, 2005
Asking For Help - Tips on where to go and how to do it.
Thursday, July 14, 2005
Oracle Docs - For when people tell you to RTFM!
Best Practises:
Tuesday, June 14, 2005
Bind Variables in PL/SQL - Short answer: PL/SQL binds all variables (with some exceptions like dynamic SQL)
Tuesday, January 24, 2006
Gathering Requirements
Wednesday, March 01, 2006
Handling exceptions - A how-to guide.
Friday, March 10, 2006
Handling Performance Issues
Wednesday, August 17, 2005
Keeping Tables Small - In terms of number of rows, not columns. Improve performance.
Monday, October 31, 2005
Oracle Packages - And why/how you should use them.
Monday, July 11, 2005
Specifying INSERT Columns - Why it's a good habit.
Wednesday, May 18, 2005
Steven Feuerstein on Refactoring
Tuesday, July 26, 2005
Use Constraints - A how-to guide for people to whom I BEG to let the database handle the data's integrity.
Monday, July 25, 2005
Use Views - Why they're handy.
Oracle Packages:
Wednesday, October 12, 2005
DBMS_OUTPUT.PUT_LINE
Thursday, November 24, 2005
DBMS_PIPE - For communication between sessions
Sunday, August 14, 2005
UTL_HTTP - Including an example of how to get a stock quote from the Internet.
For Newbies:
Tuesday, December 20, 2005
20 Beginner Oracle Questions
Friday, June 17, 2005
Asking For Help - Tips on where to go and how to do it.
Thursday, July 14, 2005
Oracle Docs - For when people tell you to RTFM!
Best Practises:
Tuesday, June 14, 2005
Bind Variables in PL/SQL - Short answer: PL/SQL binds all variables (with some exceptions like dynamic SQL)
Tuesday, January 24, 2006
Gathering Requirements
Wednesday, March 01, 2006
Handling exceptions - A how-to guide.
Friday, March 10, 2006
Handling Performance Issues
Wednesday, August 17, 2005
Keeping Tables Small - In terms of number of rows, not columns. Improve performance.
Monday, October 31, 2005
Oracle Packages - And why/how you should use them.
Monday, July 11, 2005
Specifying INSERT Columns - Why it's a good habit.
Wednesday, May 18, 2005
Steven Feuerstein on Refactoring
Tuesday, July 26, 2005
Use Constraints - A how-to guide for people to whom I BEG to let the database handle the data's integrity.
Monday, July 25, 2005
Use Views - Why they're handy.
Oracle Packages:
Wednesday, October 12, 2005
DBMS_OUTPUT.PUT_LINE
Thursday, November 24, 2005
DBMS_PIPE - For communication between sessions
Sunday, August 14, 2005
UTL_HTTP - Including an example of how to get a stock quote from the Internet.
Monday, March 27, 2006
Data Analysis
Data Analysis: "caWorkbench
caWorkbench is an extendible and flexible desktop tool for microarray data analysis and visualization. The release 1.0 includes several data analysis and visualization functions, including hierarchical clustering, self organizing maps, color mosaic images and biological pathways.'"
caWorkbench is an extendible and flexible desktop tool for microarray data analysis and visualization. The release 1.0 includes several data analysis and visualization functions, including hierarchical clustering, self organizing maps, color mosaic images and biological pathways.'"
YASMA - Yet Another Statistical Microarray Analysis
YASMA - Yet Another Statistical Microarray Analysis: "YASMA is an add-on library for the R statistical package and can be used to analyse simple replicated experiments. For example, we are interested in bacterial genes over- or under-expressed in mutants as compared to the wild type. For this purpose, multiple mRNA preparations are hybridized on several arrays. As long as the same number of arrays is used for each preparation a straightforward ANOVA analysis and analysis of variance components can be applied to the series of experiments (a balanced factorial design).
At the moment the package contains
* Routines for inspecting the correlation between array replicates and for removing low expression genes that cause low correlation.
* A method for interpolating missing data using estimates from an ANOVA analysis.
* Routines for fast ANOVA analysis of data typical for microarrays experiments (balanced factorial designs with nested factors). The design matrix for such analysis is usually very large (due to the effects involving genes) and cannot be dealt with efficiently by standard ANOVA routines based on design matrix evaluations.
* Routines for an analysis of variance components: cultures, arrays, etc are random representatives of possible experiments and need to be analyzed in a slightly different way than by simple ANOVA.
* A routine to caculate the optimal design of an experiment based on relative costs of cultures, arrays, etc, and on estimates of variability from a prior experiment.
* Calculation of p-values derived from the results of the analysis of variance components. If residuals show different amounts of variance (which is often the case), hierarchical bootstrapping of residuals is a more reliable way to derive p-values.
* Implementations of additional standard tests (t-statistic) and of Newton's et. al hierarchical model methods (see below the Statistics Notes) for multiple experiments."
At the moment the package contains
* Routines for inspecting the correlation between array replicates and for removing low expression genes that cause low correlation.
* A method for interpolating missing data using estimates from an ANOVA analysis.
* Routines for fast ANOVA analysis of data typical for microarrays experiments (balanced factorial designs with nested factors). The design matrix for such analysis is usually very large (due to the effects involving genes) and cannot be dealt with efficiently by standard ANOVA routines based on design matrix evaluations.
* Routines for an analysis of variance components: cultures, arrays, etc are random representatives of possible experiments and need to be analyzed in a slightly different way than by simple ANOVA.
* A routine to caculate the optimal design of an experiment based on relative costs of cultures, arrays, etc, and on estimates of variability from a prior experiment.
* Calculation of p-values derived from the results of the analysis of variance components. If residuals show different amounts of variance (which is often the case), hierarchical bootstrapping of residuals is a more reliable way to derive p-values.
* Implementations of additional standard tests (t-statistic) and of Newton's et. al hierarchical model methods (see below the Statistics Notes) for multiple experiments."
Saturday, March 25, 2006
eJournals
Links| eJournals: "Journals
Scope: Bioinformatics / Computational Biology"
Scope: Bioinformatics / Computational Biology"
- AMB - Algorithms for Molecular Biology
- Soon to be launched by BioMedCentral.
- Applied Bioinformatics
- - Reviews of computational and methodological developments
- Original research articles on all areas of bioinformatics including microarray analysis, databases and datamining, phylogenetics, forensics, protein structure prediction and evolution, and genomics
[Search PubMed] - Bioinformatics (formerly CABIOS)
- Main focus on new developments in genome bioinformatics and computational biology.
ISI impact factor of 5.742 (2004), 6.701 (2003), 4.615 (2002), 3.421 (2001)
[Search PubMed] - Biological Knowledge
- Forum for scientific communication regarding analysis of the content and the role of knowledge in biology and medicine. The fields covered by the journal include: ontologies, knowledge representation, and knowledge bases; reasoning, discovery, and machine learning; natural language processing and linguistics; history, philosophy, sociology, and anthropology; cognitive science, including cognitive and social psychology; and education.
Open access online journal, to be launched soon, see recent updates. - BMC Bioinformatics
- Publishes original research articles in all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology.
Open access online journal.
ISI impact factor of 5.42 (2004), 4.896 (estimated, 2003)
[Search PubMed] - Briefings in Bioinformatics
- An international forum for researchers and educators in the life sciences, Briefings in Bioinformatics publishes reviews for the users of databases and analytical tools in contemporary genetics and molecular biology.
[Publisher] - [ToC] - [Search PubMed] - Comparative and Functional Genomics
- - studies of complex and model organisms
- bioinformatic and computational tools for the study of gene and genome organisation
- pharmacogenomics and genomics-based drug target identification methods
- Computational Biology and Chemistry
- Formerly known as Computers & Chemistry
- Computer Methods and Programs in Biomedicine
- Covers computing methodology and software systems derived from computing science for implementation in all aspects of biomedical research and medical practice.
- Computers in Biology and Medicine
- Application of the computer to the fields of biomedical engineering and medical informatics.
- Analysis of biomedical systems: solutions of equations
- Synthesis of biomedical systems: simulations
- Special medical data processing methods
- Special purpose computers and clinical data processing
- Medical diagnosis and record processing
Audience: Physicians, Surgeons, Physiologists, Bacteriologists - IJBRA - International Journal of Bioinformatics Research and Applications
- IJDMB - International Journal of Data Mining and Bioinformatics
- Launched recently
- IJMI - International Journal of Medical Informatics
- ISI impact factor of 1.326 (2004), 1.178 (2003)
Available on Science Direct
[Search PubMed] - Journal of Biomedical Informatics
- Formerly known as "Computers and Biomedical Research"
ISI impact factor of 0.855 (2003) - JBCB - Journal of Bioinformatics and Computational Biology
- Aims to publish high quality, original research articles, expository tutorial papers and review papers as well as short, critical comments on technical issues associated with the analysis of cellular information.
- JIB - Journal of Integrative Bioinformatics
- Focuses on
- molecular biological databases and applications
- integration of data sets relevant for biological systems
- integration of applications relevant for biological systems
- design of metabolic, regulatory and expression networks
- interdisciplinary studies of these networks
- evaluation of original experimental data with biocomputational tools
- online resources for experimental scientists - JCB - Journal of Computational Biology
- Forum for the communication of technical issues associated with the analysis, management, and visualization of cellular information at the molecular level. Includes papers on genomics, mathematical modeling and simulation, distributed and parallel biological computing, designing biological databases, pattern matching and pattern detection, linking disparate databases and data, new tools for computational biology, relational and object-oriented database technology for bioinformatics, biological expert system design and use, reasoning by analogy, hypothesis formation and testing by machine, and management of biological databases
ISI Impact Factor of 4.600 (2003) - JTB - Journal of Theoretical Biology
- The forum for theoretical papers that give insight into biological processes.
ISI Impact Factor of 1.550 (2003)
[Search PubMed] - LNCS Transactions on Computational Systems Biology
-
- OJB - Online Journal of Bioinformatics
-
- PloS Computational Biology
- Open access, launched in June 2005.
[Search PubMed]
Scope: Machine Learning
Electronic Journals Library
Electronic Journals Library: "Search results"
- Applied Bioinformatics
- Bioinformatics
- Bioinformatics (1996 - älter als 12 Monate)
- BMC Bioinformatics Briefings in Bioinformatics
- Current Protocols in Bioinformatics
- Evolutionary Bioinformatics
- EEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
- International Journal of Bioinformatics Research and Applications
- Journal of Bioinformatics and Computational Biology (JBCB)
- Journal of Integrative Bioinformatics (JIB)
- Online Journal of Bioinformatics (OJB)
- Proteins: Structure, Function, and Bioinformatics (1996 -)
- Journal of Machine Learning Research (JMLR)
- Journal of Machine Learning Research (JMLR)
- Machine Learning
Friday, March 24, 2006
MIT OpenCourseWare | Electrical Engineering and Computer Science | 6.867 Machine Learning, Fall 2002 | Tools
MIT OpenCourseWare | Electrical Engineering and Computer Science | 6.867 Machine Learning, Fall 2002 | Tools: "MATLAB® is a computational environment (language and tools) designed primarily for numerical computation and manipulation. It is very useful for running Machine Learning experiments, and we will be using it extensively for this course.
MIT Information Systems also provides some useful tips for a beginning MATLAB® user."
Resources
· MATLAB® at MIT
· Mathworks' MATLAB® documentation
· UNH MATLAB® Tutorial
· US Navy MATLAB® Tutorial
· MTU Introduction to MATLAB®
MIT Information Systems also provides some useful tips for a beginning MATLAB® user."
Resources
· MATLAB® at MIT
· Mathworks' MATLAB® documentation
· UNH MATLAB® Tutorial
· US Navy MATLAB® Tutorial
· MTU Introduction to MATLAB®
MATLAB® is a trademark of The MathWorks, Inc.
Peter's R Programming Pages
Peter's R Programming Pages: "R is a language and environment for statistical computing and graphics, available for free from The R Project. It is very similar to the S language and its commercial derivative, S-PLUS.
Have a look at this R Graph Gallery for an idea of the sort of images R can create.
If you are working with microarray data then you should really look at the Bioconductor package, a set of freely available biologically useful statistical tools."
Have a look at this R Graph Gallery for an idea of the sort of images R can create.
If you are working with microarray data then you should really look at the Bioconductor package, a set of freely available biologically useful statistical tools."
RankGene Home Page
RankGene Home Page: "Rankgene: a program to rank genes from expression data
Yang Su, T. M. Murali, Vladimir Pavlovic, Mike Schaffer, and Simon Kasif"
Yang Su, T. M. Murali, Vladimir Pavlovic, Mike Schaffer, and Simon Kasif"
BioWarehouse Software Overview
BioWarehouse Software Overview: "BioWarehouse – Database Integration for Bioinformatics
V3.5 6/21/2005
Overview
BioWarehouse is a component of the Bio-SPICE project. BioWarehouse is an open-source software environment for integrating a set of biological databases into a single physical database management system for data management, mining, and exploration.
Key features of BioWarehouse:
* A relational database schema that models important bioinformatics datatypes
* BioWarehouse instances can be implemented using either the Oracle or MySQL database management systems
* A collection of loader programs that populate the warehouse with data from public biological databases
* The loader programs transform the syntax of the source databases into relational form, and transform the diverse semantics of the source database into the common semantics of the BioWarehouse schema.
BioWarehouse Loaders"
V3.5 6/21/2005
Overview
BioWarehouse is a component of the Bio-SPICE project. BioWarehouse is an open-source software environment for integrating a set of biological databases into a single physical database management system for data management, mining, and exploration.
Key features of BioWarehouse:
* A relational database schema that models important bioinformatics datatypes
* BioWarehouse instances can be implemented using either the Oracle or MySQL database management systems
* A collection of loader programs that populate the warehouse with data from public biological databases
* The loader programs transform the syntax of the source databases into relational form, and transform the diverse semantics of the source database into the common semantics of the BioWarehouse schema.
BioWarehouse Loaders"
Thursday, March 23, 2006
Tutorial on DNA array data clustering
Tutorial on DNA array data clustering: "Tutorial on DNA array data clustering"
Saturday, March 18, 2006
Friday, March 17, 2006
The Scriptome - Protocols for Manipulating Biological Data
The Scriptome - Protocols for Manipulating Biological Data: "The Scriptome - Protocols for Manipulating Biological Data
The Scriptome is a set of tools that filter, format, and merge data in tabular or common biological formats. Use single tools to take a quick look at data, or string tools together in a protocol to explore the data more deeply."
The Scriptome is a set of tools that filter, format, and merge data in tabular or common biological formats. Use single tools to take a quick look at data, or string tools together in a protocol to explore the data more deeply."
The Scriptome was designed especially for non-programmers or beginning programmers, although more experienced programmers may find the site useful as a data manipulation "cookbook". The tools can be used without understanding them. Alternatively, you might find that reading and playing with small, working code examples - and using them on your own data - is a good way to learn Perl.
If you don't want to read the extensive help, take a text file and add line numbers to it with calc_line_numbers (from the Calc page). Or change a FASTA file to tabular format using change_fasta_to_tab (from the Change page). Also, see the example that follows each tool.
Thursday, March 16, 2006
Installing Oracle on Suse 10
Dizwell Informatics - Installing Oracle on Suse 10: "Installing Oracle on Suse 10"
Installing Oracle on Ubuntu
Dizwell Informatics - Installing Oracle on Ubuntu: "Installing Oracle on Ubuntu"
Wednesday, March 15, 2006
OPAL (Oracle PHP Apache Linux)
Linux World - Sydney Australia: "Lets Go Oracle & PHP - Deploy & Develop OPAL (Oracle PHP Apache Linux)
Get help installing Oracle Database 10/g/ Release 2 on Linux. Bring your laptop (512MB minimum) and walk away with a complete enterprise Oracle & PHP environment with Zend Core for Oracle
Get FREE software from Novell, Red Hat, and Oracle. Oracle experts will demonstrate best practices for Oracle & PHP, and interoperability with SQL, Java, and BPEL while taking advantage of PHP's explosive growth and new functionality."
Get help installing Oracle Database 10/g/ Release 2 on Linux. Bring your laptop (512MB minimum) and walk away with a complete enterprise Oracle & PHP environment with Zend Core for Oracle
Get FREE software from Novell, Red Hat, and Oracle. Oracle experts will demonstrate best practices for Oracle & PHP, and interoperability with SQL, Java, and BPEL while taking advantage of PHP's explosive growth and new functionality."
apache friends - xampp for linux faq
apache friends - xampp for linux faq: "To activate the OCI8/Oracle extension for PHP please execute the following command:
/opt/lampp/lampp oci8
The following dialog will start:"
Please enter the path to your Oracle installation:
ORA_HOME [/opt/oracle/OraHome1]
installing symlinks...
patching php.ini...
OCI8 add-on activation likely successful.
LAMPP: Stopping Apache with SSL...
LAMPP: Starting Apache with SSL...
/opt/lampp/lampp oci8
The following dialog will start:"
Please enter the path to your Oracle installation:
ORA_HOME [/opt/oracle/OraHome1]
installing symlinks...
patching php.ini...
OCI8 add-on activation likely successful.
LAMPP: Stopping Apache with SSL...
LAMPP: Starting Apache with SSL...
Now the extension should be active
Tuesday, March 14, 2006
Decision tree - Wikipedia, the free encyclopedia
Decision tree - Wikipedia, the free encyclopedia: "In decision theory, a decision tree is a graph of decisions and their possible consequences, (including resource costs and risks) used to create a plan to reach a goal. Decision trees are constructed in order to help with making decisions. A decision tree is a special form of tree structure."
Phylogenetic Biology (BIOS 429/829)
Phylogenetic Biology (BIOS 429/829): "Phylogenetic Biology, BIOS 429/829"
Biotech: Bioinformatics
Biotech: Bioinformatics
Online Bioinformatics Courses: The development of bioinformatics courses is still in its infancy. Only a few universities around the world offer courses specifically designed for this field. Following are the few online courses in bioinformatics currently accessible, two of which represent hypertext editions of university courses.
Online Bioinformatics Courses: The development of bioinformatics courses is still in its infancy. Only a few universities around the world offer courses specifically designed for this field. Following are the few online courses in bioinformatics currently accessible, two of which represent hypertext editions of university courses.
Algorithms in Molecular Biology - Ron Shamir - Course Archive
Algorithms in Molecular Biology - Ron Shamir - Course Archive: "This archive contains material of the course 'Algorithms for Molecular Biology', taught by Ron Shamir "
Monday, March 13, 2006
SynBrowse
SynBrowse: "SynBrowse (Synteny Browser) is a generic sequence comparison tool for visualizing genome alignments both within and between species. It is intended to help scientists study and analyze synteny, homologous genes and other conserved elements between sequences. This software is useful in studying genome duplication and evolution. It can also aid in identifying uncharacterized genes, putative regulatory elements and novel structural features of study species by comparing to a well annotated reference sequence, thus enabling genome curators to refine and edit annotations of species that have incomplete genome annotations."
MDCalc, The Clinical Calculator.
MDCalc, The Clinical Calculator.: "Quick access to medical calculations.
Start spending more time diagnosing, and less time dividing"
Start spending more time diagnosing, and less time dividing"
BioMart Project
BioMart Project: "BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL).
The system can be used with any type of data and comes with a range of query interfaces and administration tools, including 'out of the box' website that can be installed, configured and customised according to requirements. The system simplifies the task of creation and maintenance of advanced query interfaces backed by a relational database and it is particularly suited for providing the 'data mining' like searches of complex descriptive (e.g. biological) data. BioMart can work with existing data repositories by converting them to a required BioMart format as well as newly created databases. "
The system can be used with any type of data and comes with a range of query interfaces and administration tools, including 'out of the box' website that can be installed, configured and customised according to requirements. The system simplifies the task of creation and maintenance of advanced query interfaces backed by a relational database and it is particularly suited for providing the 'data mining' like searches of complex descriptive (e.g. biological) data. BioMart can work with existing data repositories by converting them to a required BioMart format as well as newly created databases. "
The Generic Model Organism Database Project | GMOD
The Generic Model Organism Database Project | GMOD: "The Generic Model Organism Database (GMOD) Project is a largely open source project to develop a complete set of software for creating and administering a model organism database. Components of this project include genome visualization and editing tools, literature curation tools, a robust database schema, biological ontology tools, and a set of standard operating procedures. This project is funded by the NIH and the USDA Agricultural Research Service, with participation from members of several database projects, including WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database."
GUS: The Genomics Unified Schema
GUS: The Genomics Unified Schema:
"GusSchema 3.5.1, a patch release is now available from the subversion repository for use with the latest install and GusAppFramework packages. Upgrade scripts and instructions are included. Also, a stand-alone SchemaBrowser written by Conrad Ibanez and collaborators at the University of Georgia is now available for download."
The Genomics Unified Schema (GUS) is an extensive relational database schema and associated application framework designed to store, integrate, analyze and present functional genomics data. The GUS schema supports a wide range of data types including genomics, gene expression, transcript assemblies, proteomics and others. It emphasizes standards-based ontologies and strong-typing.
The GUS Application Framework offers an object-relational layer and a Plugin API used to rapidly create robust data loading programs for diverse data sources. The GUS distribution includes plugins for standard data sources. The GUS Web Development Kit (WDK) is a rich environment for efficiently designing sophisticated query-based websites with little programming required.
"GusSchema 3.5.1, a patch release is now available from the subversion repository for use with the latest install and GusAppFramework packages. Upgrade scripts and instructions are included. Also, a stand-alone SchemaBrowser written by Conrad Ibanez and collaborators at the University of Georgia is now available for download."
VBI MICROBIAL DATABASES
VBI MICROBIAL DATABASES: "The microbial database at VBI hosts data from a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at the VBI. The data comes from different sources. Click here for more information.For some of the oomycetes e.g; Phytophthora sojae, EST,genome sequence and microaray data are stored. The database is powered by GUS"
EST Database
EST Database: "Phytophthora ESTs
Phytophthora species are stramenopiles, and belong to a kingdom distinct from plants, fungi, and animals that also includes diatoms and brown algae. No stramenopile genomes have yet been sequenced."
Phytophthora species are stramenopiles, and belong to a kingdom distinct from plants, fungi, and animals that also includes diatoms and brown algae. No stramenopile genomes have yet been sequenced."
Wednesday, March 08, 2006
Use two monitors for greater productivity
USATODAY.com - Use two monitors for greater productivity: "You can add memory and lessen your system's load to increase your computer's performance. But if you want to improve your productivity, add a second monitor. Researchers at Microsoft found that workers increased their productivity 9% to 50% by adding a second or third monitor."
Tuesday, March 07, 2006
JavaScript arrays: combining and splitting
JavaScript arrays: combining and splitting: "How to combine or join all elements available in an array using JavaScript"
WebArray - Online Microarray Data Analysis Platform
WebArray - Online Microarray Data Analysis Platform
WebArray is a web platform for analysis of microarray data. The computations are powered by R language and Bioconductor. Benefited from Bioconductor, WebArray is able to deal with intensity data files of many different types, like Affymetrix, Agilent, Genepix, QuantArray, etc. WebArray offers many conventional functions for microarray data analysis:
- Background Substration Including several methods.
- Normalization For within-array normalization, methods cover print-tip loess, global loess, median, robust spline; for between-array normalization, methods include Aquantile, Gquantile, PCA, Quantile, Rquantile, Scale and vsn.
- Analysis limma-based linear model statistical analysis (including FDR calculation with SPLOSH).
- Genome Mapping Available for different genome types.
Monday, March 06, 2006
paloverde
paloverde:
Paloverde v. 1.1
A 3-D tree visualization tool
This is a simple program to do three-D visualizations of moderately large phylogenies. Trees with between 100 and 2500 taxa seem to work best (more if subclades are defined by the user). Faster graphics hardware than is available by default on my Powerbook G4 laptop extend the range upward, as does a large "cinema" display.
Paloverde v. 1.1
A 3-D tree visualization tool
This is a simple program to do three-D visualizations of moderately large phylogenies. Trees with between 100 and 2500 taxa seem to work best (more if subclades are defined by the user). Faster graphics hardware than is available by default on my Powerbook G4 laptop extend the range upward, as does a large "cinema" display.
PAL: Phylogenetic Analysis Library
The PAL Project:
"PAL: Phylogenetic Analysis Library
Main Features:
PAL is entirely written in the Java language. This allows for a clean object oriented design while avoiding the complexities of C++. Moreover, Java class code runs without needing recompilation on a wide range on platforms. Additionally, PAL also compiles into native code on Unix systems (just like C++) using the GNU compiler for Java (gcj), part of recent releases of the GNU compiler collection (gcc). Corresponding makefiles are included with this distribution of PAL.
PAL consists of a rich variety of objects to facilitate the construction of special-purpose tools for phylogenetic analysis. PAL contains, e.g., ready-to-use objects for:
* reading and writing sequence alignments, distance matrices, and trees
* a large variety of substitution models for nucleotides and amino acids (REV, TN, HKY, F84, F81, JC; Dayhoff, JTT, MTREV24, BLOSUM, VT, WAG, CPREV) as well as for codons (Yang codon model)
* Various models for rate variation over sites (invariable sites, Gamma)
* efficient maximum-likelihood estimation of pairwise distances and of branch lengths in a tree (for unconstrained, clock, and dated-tips clock trees)
* simulating coalescence intervals and estimation of demographic parameters
* likelihood ratio and chi-square tests and for comparison of phylogenetic hypotheses (e.g., Kishino-Hasegawa and Shimodaira-Hasegawa tests)
* manipulating alignments (e.g., bootstrapping) and trees and simulating data
* optimizing uni- and multivariate functions by various methods, computing numerical derivatives, random numbers (simulation quality), sorting etc.
* creating formatted input and output from/to files, standard io streams, and strings, through convenience classes that extend the standard Java IO library
* construct neighbor-joining, UPGMA and SUPGMA trees, and estimating least-squares branch lengths on trees (weighted and unweighted LS)
"
"PAL: Phylogenetic Analysis Library
Main Features:
PAL is entirely written in the Java language. This allows for a clean object oriented design while avoiding the complexities of C++. Moreover, Java class code runs without needing recompilation on a wide range on platforms. Additionally, PAL also compiles into native code on Unix systems (just like C++) using the GNU compiler for Java (gcj), part of recent releases of the GNU compiler collection (gcc). Corresponding makefiles are included with this distribution of PAL.
PAL consists of a rich variety of objects to facilitate the construction of special-purpose tools for phylogenetic analysis. PAL contains, e.g., ready-to-use objects for:
* reading and writing sequence alignments, distance matrices, and trees
* a large variety of substitution models for nucleotides and amino acids (REV, TN, HKY, F84, F81, JC; Dayhoff, JTT, MTREV24, BLOSUM, VT, WAG, CPREV) as well as for codons (Yang codon model)
* Various models for rate variation over sites (invariable sites, Gamma)
* efficient maximum-likelihood estimation of pairwise distances and of branch lengths in a tree (for unconstrained, clock, and dated-tips clock trees)
* simulating coalescence intervals and estimation of demographic parameters
* likelihood ratio and chi-square tests and for comparison of phylogenetic hypotheses (e.g., Kishino-Hasegawa and Shimodaira-Hasegawa tests)
* manipulating alignments (e.g., bootstrapping) and trees and simulating data
* optimizing uni- and multivariate functions by various methods, computing numerical derivatives, random numbers (simulation quality), sorting etc.
* creating formatted input and output from/to files, standard io streams, and strings, through convenience classes that extend the standard Java IO library
* construct neighbor-joining, UPGMA and SUPGMA trees, and estimating least-squares branch lengths on trees (weighted and unweighted LS)
"
Mayday
Mayday: "Mayday - A microarray data analysis framework
Mayday is a workbench for visualization, analysis and storage of microarray data. It features a graphical user interface and supports the development and integration of existing and new analysis methods. Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods. In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources, which is a feature that, for instance, is employed in the enhanced heatmap visualization.
Written in the Java programming language, Mayday is extremely portable and runs on all platforms supporting the Java runtime environment 1.5 (for the current 2.0 release) or 1.4.1 and later (for the 1.0-1.1 releases)."
Mayday is a workbench for visualization, analysis and storage of microarray data. It features a graphical user interface and supports the development and integration of existing and new analysis methods. Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods. In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources, which is a feature that, for instance, is employed in the enhanced heatmap visualization.
Written in the Java programming language, Mayday is extremely portable and runs on all platforms supporting the Java runtime environment 1.5 (for the current 2.0 release) or 1.4.1 and later (for the 1.0-1.1 releases)."
SimArray: a user-friendly and user-configurable microarray design tool - Home
SimArray: a user-friendly and user-configurable microarray design tool - Home:
"Background
Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic.
Results
We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and an estimated print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; microtitre plate format; pin configuration, and achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.
Conclusion
SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. The source code is available from this web site."
"Background
Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic.
Results
We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and an estimated print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; microtitre plate format; pin configuration, and achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.
Conclusion
SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. The source code is available from this web site."
Dev Articles - Java
DEV ARTICLES _ Java
"Java Code, Java Design, Java Tools, Java Info, and more! Dev Articles contains tutorials, articles, code samples, and other various resources. Our writings feature in-house authors, freelance writers, and several exclusive publishing relationships."
"Java Code, Java Design, Java Tools, Java Info, and more! Dev Articles contains tutorials, articles, code samples, and other various resources. Our writings feature in-house authors, freelance writers, and several exclusive publishing relationships."
Designing Your own XML Schema: Learn the Essentials
Designing Your own XML Schema: Learn the Essentials:
What is XML Schema and why does it exist?
XML documents (or files with the extension “.xml”) are designed with no rules and regulations by default. Don’t be misled by the phrase “no rules and regulations.” In this sense, I mean that it is “highly customizable.” That means no one in this world can constrain or stop you from defining your own “markup” language. You can start with your own elements, attributes, and values along with your own structure.
What is XML Schema and why does it exist?
XML documents (or files with the extension “.xml”) are designed with no rules and regulations by default. Don’t be misled by the phrase “no rules and regulations.” In this sense, I mean that it is “highly customizable.” That means no one in this world can constrain or stop you from defining your own “markup” language. You can start with your own elements, attributes, and values along with your own structure.
Sunday, March 05, 2006
PANTHER - Classifications of Genes and Proteins
PANTHER - Classifications of Genes and Proteins: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms. For an increasing number of proteins, detailed biochemical interactions in canonical pathways are captured and can be viewed interactively."
ArrayTrack Microarray database and analysis software
NCTR Center for Toxicoinformatics - ArrayTrack Microarray database and analysis software: "ArrayTrack provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, ArrayTrack is MIAME (Minimum Information About A Microarray Experiment) supportive for storing both microarray data and experiment parameters associated with a pharmaco- or toxico- genomics study. Many statistical and visualization tools are available with ArrayTrack. ArrayTrack also provides a rich collection of functional information about genes, proteins and pathways for biological interpretation. The primary emphasis of ArrayTrack is the direct linking of analysis results with functional information for facilitating the interaction between the choice of analysis methods and the biological relevance of analysis results. Using ArrayTrack, user can easily select a statistical method applied to a stored microarray data to determine a list of differentially expressed genes and the gene list can be directly linked to pathways and gene ontology for functional analysis."
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