Bioinformatics/Neuroinformatics

About Bioinformatics

[Under Construction - Will be available at a later date.]

Download Bioinformatics Files

Students and Faculty can download the Image J Program (which runs the Bioinformatics module) and Bioinformatics Tutorials for free.

1.  Download the Image J Program (from the NIH Website):

• Image J

2.  Download the 'All Mice' folder, the complete set of images (taken from the MBL Website):

• All Mice v1.0 (Image Library - .zip format)

3.  Take the Student Pre-Test:  If you are a student and are about to begin the Bioinformatics module, please provide us with your level of scientific knowledge going into the module by taking the following Pre-Tests.  In order to access the Pre-Test, you must first fill out the User Consent/Download Questionnaire (after which you will be directed to the link).  Note that you will still be allowed to access the Pre-Test even if you choose NOT to consent to anything.

• Student Pre-Test

4.  Download the Bioinformatics Tutorials:  In order to access the Tutorials Folder, you must first fill out the User Consent/Download Question (after which you will be directed to the download folder).  Note that you will still be allowed to download the tutorials even if you choose NOT to consent to anything.

Download the Tutorials now:

• Download Tutorials

Included in the Tutorials Folder are the following files:

• Complete Users Manual (.pdf for both students and instructors)

• Tutorial Part 1 of 8:  Using Image J to Measure Olfactory Bulb Volume  (.pdf)

• Tutorial Part 2 of 8:  Using Image J to Measure Whole Brain Volume  (.pdf)

• Tutorial Part 2 of 8 Supplement:  Template with Mouse Demographics for Collected Data (.xls)

• Tutorial Part 3 of 8:  Using SPSS to Run Regression (.pdf)

• Tutorial Part 3 of 8 Supplement:  Template with Averaged Residuals for Statistical Data  (.xls)

• Tutorial Part 4 of 8:  Using Genenetwork/WebQTL to Analyze Trait Data  (.pdf)

• Tutorial Part 4 of 8 Supplement:  List of BxD Markers (.xls)

                last updated:  03-26-09

• Tutorial Part 5 of 8:  Using UCSC Genome Browser to Find Genes  (.pdf)

• Tutorial Part 6 of 8:  Using Allen Brain Atlas to Find Gene Expression  (.pdf)

• Tutorial Part 7 of 8:  Using Entrez Gene to Find Full and Coding Sequences  (.pdf)

• Tutorial Part 8 of 8:  Using PubMed to Find Related Articles  (.pdf)

                last updated:  09-22-09

5.  Take the Student Post-Test:  If you are a student and have completed the Bioinformatics module, please provide us with your level of scientific knowledge coming out of the module by taking the following Post-Test.  In order to access the Post-Test, you must first fill out the User Consent/Download Questionnaire (after which you will be directed to the link).  Note that you will still be allowed to access the Post-Test even if you choose NOT to consent to anything.

• Student Post-Test
  

6.  Fill out the Student Materials Evaluation:  If you are a student and have completed the Bioinformatics module, please provide us with basic feedback on the materials used in this module by filling out the multiple choice Student Materials Evaluation.  In order to access the Materials Evaluation, you must first fill out the User Consent/Download Questionnaire (after which you will be directed to the link).  Note that you will still be allowed to access the Materials Evaluation even if you choose NOT to consent to anything.

• Student Materials Evaluation

For Faculty

Faculty members interested in accessing faculty-related materials will need to obtain an account.  Please see the Faculty Web Page for more information.  Faculty members that already have an account may log in and go directly to the Faculty Bioinformatics Web Page.

If you are a faculty member that has individually completed or taught the SWIMMY Module, please provide us with basic feedback on the materials used in this module by filling out the multiple choice Faculty Materials Evaluation:

• Faculty Materials Evaluation

Extras

• Image of Measured Olfactory Bulb  (large image detailing regions to select in Image J)
• Sample Data (previously acquired data to be used for practice)

• Bioinformatics FAQ
• mdcune.ucla@gmail.com (please put "Bioinformatics Question" in the subject line)

Related Links

• NIH Image
• Scion Corporation for free imaging software
• Mouse Brain Library
• GeneNetwork/WebQTL
• UCSC Genome Browser
• Allen Brain Atlas
• NCBI Entrez Gene
• NCBI PubMed

License Information