September 30, 2009

Where can I access SAS, SPSS and other statistical software?

Stanford affiliates can access SAS, SPSS, MatLab, GraphPad Prism, and SYSTAT for statistical manipulation via computers in Lane Library's Redwood Room and Duck Room and in the M206 PC Teaching Lab.


First time users need to check in with Minmin Qin in M222A, to learn how to use the key server for these programs. Once this is done, you can use them on any of our Stanford-only computers (i.e., you need to have a SUNet ID).


All statistical programs are listed in the Lane Catalog; to discover all the programs that are available, enter these Keywords:
+statistics +software


For all statistical software at Lane, see Lane Applications.


In addition, you can use statistical software, statistical datasets, and get expert help at Green Library in the SSRC (Social Sciences Research Center).

Statistics consulting is available from the Statistics Department and from SPCTRM.


Updated 6/19/2007.

Posted by mtinsley at 01:42 AM | Comments (0)

September 29, 2009

What computer and software manuals are available at Lane?

The Lane Library provides access to many software and computer manuals online via Safari and 24/7. Try searching for either the topic (e.g., UNIX) or the book title in the LaneConnex search box; when results are displayed, select a relevant title or click on the tab for e-Books. You can also browse by publisher and package or series. Manuals for working with MS Office 2007 are available in the Redwood Room for ready reference.

Go to the eBooks page and click on the title of the collection (e.g., Safari Books Online at Stanford) to search and read the content of the books.

Topics include Linux, UNIX, HTML, XML, Dreamweaver, SQL, Apache, Perl, Excel, Access, Outlook, Flash, and many more.

Posted by mtinsley at 01:47 AM | Comments (0)

May 18, 2009

What is the BOV BLAST visualizer?

What is it?

The BLAST Output Visualization Tool (BOV) enables users to interactively visualize BLAST high-scoring segment pairs to understand matching patterns between a query and a subject sequence using a Web browser.

BOVPic3.png

What is it for?

BOV uses the output from the BLAST program to understand the properties of BLAST alignments that can be made between two sequences, such as:

How to use it

A BLAST output file is uploaded to the BOV site, which then generates alignment diagrams in real-time. If desired, an e-mail address can be submitted such that a URL pointing to the results will be forwarded to user. The URL can be used to access the results for 60 days.

Unique characteristics

BOV's software is open source and can be installed locally on a Linux machine. It relies on Perl (including BioPerl modules), CGI, the MySQL database and the Apache web server are used. In particular, BOV is written in such a way that users can realistically expect to be able modify it to fit specific needs, given decent programming skills.

Key references

Source

Lane Librarian

Record created 5/18/2009.

Posted by ypouliot at 02:15 PM | Comments (0)

May 05, 2009

What is RapidMiner?

What is it?

The Community Edition of RapidMiner (formerly "Yale") is an open source toolkit for data mining. Its strengths reside in part in its ability to easily define analytical steps (especially when compared with R), and in generating graphs more easily than e.g., R, or more effectively than MS Excel.

Fig1Small.png

What is it for?

RapidMiner is well suited for analyzing data generated by high-throughput instruments, e.g., genotyping, proteomics, and mass spectrometry.

Example applications: Notable selected features of RapidMiner:

How does it work?

RapidMiner provides a GUI to design an analytical pipeline (the "operator tree" in RapidMiner parlance). The GUI generates an XML (eXtensible Markup Language) file that defines the analytical processes the user wishes to apply to the data. This file is then read by RapidMiner to run the analyses automatically.

While these are running, the GUI can also be used to interactively control and inspect running processes.

Other ways of using RapidMiner involve calling RapidMiner from e.g., a Perl program. The Java application programming interface ("API") provides clear interfaces for applying operators individually (i.e., no need to create an operator tree), providing the ability to bypass the GUI and controlling analytical processes directly.

Last, you can also call individual RapidMiner functions directly from the command line.

Where to get it?

Because RapidMiner runs on Java, it can be installed on any computer on which Java runs. You can download the Community Edition of RapidMiner can be downloaded here. Note that a commercial version is also available.

Documentation

RapidMiner is well documented, especially its tutorial.

Key references

Source

Lane Librarian

Record created 5/5/2009.

Posted by ypouliot at 11:11 AM | Comments (0)

February 23, 2009

What is Galaxy?

What is it?

Developed by The Center for Comparative Genomics and Bioinformatics at Penn State, Galaxy is an innovative "metaserver" that greatly simplifies the process of genomic analysis. Its designers have gone to great lengths to save biologists from having to write programs to analyze their genomic data, a major design goal of the system and significant problem in the field.

Another major distinguishing feature is the excellent integration of the many tools and data sources needed for performing the wide array of analyses used in genome studies (described below).

What is it for?

As it names implies, Galaxy enables a very wide constellation of genomic tasks that typically involve merging, filtering or otherwise classifying genomic data. Below are a few examples of such:

What's in it?

How does it work?

Galaxy provides a common graphical interface to manipulate data sources and launch analytical programs. It also keeps the resulting datasets within a personal storage area, making it easy to keep track of what steps have been performed, since all intermediary data sets are visible.

By integrating all steps into a common interface, Galaxy largely significantly diminishes the need to learn multiple tool-specific interfaces, not to mention having to install these tools/databases locally.

Unique characteristics

The core goal of Galaxy is to facilitate analyses on genomic intervals while by eliminating the need for researchers to write the kinds of custom analytical programs required to deal with the size and complexity of genomic data files. Galaxy is one of the first metaservers to achieve this goal for genomic analysis, a significant achievement.

Noteworthy features include: Beyond its impressive functional capabilities, Galaxy is unusual in providing many excellent ultra-short video tutorials ("screencasts") to get you started quickly.

Caveats

While an impressive system, like all software Galaxy is not (yet) perfect. There have been reports that a user's "history" (the listing of steps and intermediary files) have disappeared. This is why users should always save their most important data files and manipulations locally, which Galaxy makes easy.

Need help?

Two options are available, depending on the type of question:
  1. For immediate answers to simple "point" question (e.g., "does this program run on MS Vista?"), you can contact the Bioresearch Informationist using instant messaging (Stanford affiliate only).
  2. For more involved questions, e-mail is much preferred and more likely to return a usable answer.

Key references

Source

Lane Librarian
get ultra-fast workshop notifications:http://twitter.com/LANEBIORESEARCH

Posted by ypouliot at 02:48 PM | Comments (0)

January 09, 2009

What is ProPhylER?

What is it?

ProPhylER is a tool for visualizing the evolutionary constraints that have influenced a protein, as inferred from comparative analyses of closely related proteins sequences. Most interestingly, it can display the degree of evolutionary pressure experienced by different regions of a protein.

mcadexample.png

What is it for?

ProPhylER is an impressive tool for tasks such as:

What's in it?

ProPhylER provides precomputed visual reports of the evolutionary constraints and physicochemical properties of eukaryotic proteins.

How does it work?

The protein sequence of known orthologs/paralogs are aligned together to generate phylogenetic trees that are used to assess the sequence variability of individual positions against the backdrop of species divergence, as described here. This is done in a batch manner, so all the user needs to do is find the cluster that includes the protein of interest.

This can be done using:

Bear in mind

Key references

Source

Lane Librarian
get ultra-fast workshop notifications:http://twitter.com/LANEBIORESEARCH

Posted by ypouliot at 02:33 PM | Comments (0)

November 17, 2008

eBook reading station

eBook reading station

It is difficult to read books online on small screens, which is why Lane Library has set up an eBook Reading Station in the Stone Room (See the Stone Room floorplan). You will need to log in with your SUNet ID and password to use it.

The eBook Reading Station PC is the same as other Lane public computers with: