Computing and Mathematics Across the Sciences

A. Malcolm Campbell & Laurie J. Heyer

General Biology

Sickle Cell Disease mutagenesis page (see the consequence of a base change)

CFTR web exercise (learn about protein that causes cystic fibrosis)

Huntington Disease web exercise (hunt for the gene)

Kyte-Doolittle hydropathy plots (predict which proteins are integral membrane proteins)

Genomics, Proteomics and Systems Biology Course

Course web page (syllabus, daily schedule, old tests, etc.)

Student web pages (assigned for grades in genomics class)

Textbook web site (many free links, methods, activities, etc.)

Laboratory Methods in Genomics Lab Course

Genome annotation course web page (syllabus, daily schedule, assignments, links to papers, etc.)

Genome annotation course wiki (student-written wiki pages that culminated in a paper submission to PLoS ONE)

JGI genomics education (provides tools and training for annotating microbial genomes with students)

Genomics Education Partnership (provides tools and training for annotating fly genomes with students)

Phage Hunting at HHMI (provides tools and training for isolating and identifying non-pathogenic phage genomes)

GCAT and DNA Microarrays

GCAT web site (Main web site for undergraduate DNA microarrays)

What are DNA microarrays? Short animation. Longer but very good animation.

DNA microarray wet lab simulation and math module (Carolina Biological distributes this kit - inexpensive, works every time, learning gains demonstrated)

Spot synthesizer (produce tiff files with two color ratios that you determine - great for training, practicing, or testing)

Real time clustering web site (learn how clustering works, guided tutorial on how to use it)

Correlation Spreadsheet file (learn how correlation works and get a gut feeling for it - interactive and real-time responses)

MAGIC Tool (free access software, Mac/Windows/Linux, analyze microarray data, very powerful and FREE)

Full microarray protocols (wet lab protocols for many different species)

Synthetic Biology

What is synthetic biology? (web site with explanations, links to papers, and PowerPoint presentation)

Synthetic biolgy seminar course web site (syllabus, daily schedule, papers, student presentations, etc.)

BioMath Connections (weekly gathering of biology and math students, links to research talks, etc.)

Wet lab protocols (our research lab protocols)

Bioinformatic tools for synthetic biology (tools developed by students for synthetic biology research)

Viz-A-Brick visualization tool (interactive way to view database of BioBrick parts)

GCAT-alog freezer stock database (you can download and install locally)

iGEM web site (Yearly competition for undergraduates from around the world)

BioMath Collaboration Questions

These problems requires collaboration between biology and math or computer science. Challenging, real-world problems you cannot solve alone.