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Bioinformatics/Neuroinformatics

Image library, student manual, and links to resources to quantify brain phenotype and perform a Quantitative Trait Locus analysis linking variation in the phenotype with chromosomal loci.

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About Bioinformatics

This module is a completely computer-based introduction to bioinformatics resources.  This easy-to-adopt module weaves together several important bioinformatic tools so students can grasp how each is used in answering research questions.  Students integrate information gathered from a website dedicated to the mouse brain (Mouse Brain Library), Quantitative Trait Locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (UCSC Genome Browser, NCBI Entrez Gene, and Allen Brain Atlas), and an information resource (PubMed).

Instructors can use these various websites in concert to introduce bioinformatic resources, as well as to teach the following: genetics from the phenotypic level to the molecular level, aspects of neuroanatomy and histology, statistics, QTL analysis, and molecular biology (including in situ hybridization and microarray analysis).

As a result, students will: discover the region(s) of the chromosome(s) influencing the phenotypic trait, generate a list of candidate genes (narrowed by expression data, find the in situ pattern of a given gene in the region of interest, look up the nucleotide sequence of the candidate gene, and find articles describing the gene.

Read the published article (from CBE--Life Sciences Education, Summer 2010, 9:98-107) about using free online resources to teach bioinformatics and neuroinformatics:

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):

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

(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:

Included in the Tutorials Folder are the following files:

  • Complete Users Manual (.pdf for both students and instructors)
                last updated:  08-27-09
  • Tutorial Part 1 of 8:  Using Image J to Measure Olfactory Bulb Volume  (.pdf)
                last updated:  09-21-09
  • Tutorial Part 2 of 8:  Using Image J to Measure Whole Brain Volume  (.pdf)
                last updated:  09-21-09
  • Tutorial Part 2 of 8 Supplement:  Template with Mouse Demographics for Collected Data (.xls)
                last updated:  09-08-09
  • Tutorial Part 3 of 8:  Using SPSS to Run Regression (.pdf)
                last updated:  09-21-09
  • Tutorial Part 3 of 8 Supplement:  Template with Averaged Residuals for Statistical Data  (.xls)
                last updated:  01-11-11
  • Tutorial Part 4 of 8:  Using Genenetwork/WebQTL to Analyze Trait Data  (.pdf)
                last updated:  01-11-11
  • 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)
                last updated:  09-22-09
  • Tutorial Part 6 of 8:  Using Allen Brain Atlas to Find Gene Expression  (.pdf)
                last updated:  09-22-09
  • Tutorial Part 7 of 8:  Using Entrez Gene to Find Full and Coding Sequences  (.pdf)
                last updated:  09-22-09
  • Tutorial Part 8 of 8:  Using PubMed to Find Related Articles  (.pdf)

                last updated:  09-22-09

(5)  View Lecture and Lab Materials:  The following are PowerPoint files that should serve as a guide to Bioinformatics instruction.  Each lecture, taught by Dr. William Grisham (UCLA), is available with and without voiceover.  Labs 2 and 3 have been combined into a single file; they can be combined and taught as a single lesson, or they can be split into two lab classes.

Lecture 1:

Lecture 2:

Lecture 3:

Lab 1:

Lab 2 and Lab 3:

(6)  Watch the lectures:  If you would like to view a series of lectures given by the teacher and developer of the Bioinformatics/Neuroinformatics module, please follow the links below.

(7)  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

(8)  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:

which includes:

  1. original .doc versions of all Bioinformatics tutorials
  2. Bioinformatics Final Exam/Report Questions
  3. Bioinformatics Final Exam/Report Answers

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

(1)  View a large image detailing regions to select (trace and measure) in Image J:

(2)  Practice running through the Bioinformatics/Neuroinformatics module with sample data:

  • Sample Data (previously acquired data to be used for practice)
(3)  UCLA Students, Fall 2011 - SPSS Data Template (to average residuals):

(4)  Read the published article (from CBE - Life Sciences Education, Summer 2010, 9:98-107) about using free online resources to teach bioinformatics and neuroinformatics:

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License Information

Creative Commons License

 

Instructor and Student Bioinformatics Lab Manual by Dr. William Grisham is licensed under a Creative Commons Attribution-No Derivative Works 3.0 United States License.
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National Science Foundation            UCLA Office of Instructional Development

Funded by the National Science Foundation and the UCLA Office of Instructional Development