Data Cleaning and Organization: Bring me all of your big, dirty, confusing wads of excel spreadsheets and lab notebooks (or however you have it stored now). I'll go through the data with a fine tooth comb and let you know how much "quantitative" data you really have to work with. Then I'll clean it up and get it ready for the next step; importing the dataset(s) into a well designed database management system, or directly into one or more data analysis tools.

Database Design and Development: I can create custom database structures that will allow you to best analyze your data based on your unique data analysis needs. I can also use previously developed database structures if that is what the project calls for. Generally, I prefer to implement my databases using MySQL because I'm a big open source fan, but if you are already using Oracle, Sybase or PostGreSQL, I have experience working with these database management tools also.

Data Warehousing: Once the database has been designed and developed, it's ready to be populated with your data. Once populated, I can run any on the fly queries you are interested in and I can also start linking this new data with data housed in publicly available biological databases. Whether (and when/how) we make your datasets public is up to you.

Software Design and Development: I can write software (Java, Perl, JavaScript, etc.) that will allow you to access and analyze your data more effectively and efficiently. Sometimes this means developing brand new (publishable) software tools and techniques. Sometimes this just means developing an interface that allows you to more easily view/manage your datasets. Sometimes it's somewhere in between.

Data Analysis: This is the real meat and potatoes of the process. I've spent a lot of time working on data mining, hypothesis testing and linking new data with data housed in publicly available biological databases. Microarray analysis generally fits well within these categories. I am also extremely interested in learning more about predictive computational modeling.

Visualization Tools: Data Analysis goes hand in hand with Data Visualization. Cluster Analysis and MDS Plots are just a couple examples of tools and techniques I can use that will help you visualize the results of hypothesis generation and testing.

Web Design: At any point along the line, I can create a website (or desktop application if you prefer) for you to easily access your data and publish your results.

Collaboration/Training: I am always excited to collaborate on a new research plan, I am always happy to explain what I am doing (or thinking about doing), and I will always clearly document exactly what I actually do when we start implementing that plan. I am also happy to present tools and techniques to groups.

My Three Major Consulting Rules:

• When it comes to data analysis and software engineering techniques and tools, if I haven't done it before, I am always, not only willing, but very excited to learn.
• I'll always try my best to do what is best for you, the customer. Sometimes this means designing and building new analysis techniques from scratch (armed with only Perl and a stack of textbooks), sometimes this means using data analysis packages that already exist (e.g. SPSS or Primer 5).
• Whenever possible, it's ideal to start collaboration on a quantitative analytic plan at the very beginning of a project, before data collection has occurred. This avoids the all too common occurrence of wanting to test a hypothesis on a set of data, but realizing too late that it's impossible because not enough of the right kind of data was collected in the first place.

• Evolutionary Computation/Artificial Life (EC/AL)
• Emergent properties of complex adaptive systems
• Pattern recognition in complex adaptive systems
• Co-evolution in complex adaptive systems
• Transition from single to multi-cellular species (the emergence of self-awareness in decentralized systems)
• Genetic computing/Organic computing

• Using EC/AL to relate environmental variables to abundance data (microbial or other)
• Using EC/AL to model biological systems
• Traditional mathematical and computer modeling of biological systems
• Using traditional data mining, database, data analysis and statistical analysis tools and techniques in the areas of
  • Microarray analysis
  • Bioinformatics/Genomics/Proteomics
  • Biological Networks
  • Microbial ecology
  • Population biology

Presently I am working on a data warehouse ultimately intended to house all public cultured species of the Aquificales Order for the Reysenbach Lab at Portland State University. The Aquificales Data Warehouse recently went live, and comments and constructive criticism are much welcome. I'm also gearing up to start some serious microarray data analysis in the very near future.

I also have research assistanceship to study coevolutionary learning with the Mitchell Research Group in the Computer Science department at Portland State.

Coevolution web page

• Email: jennifercwd at yahoo dot com (You know the get around drill.)
• Cell Phone: (503) 703-4063

Includes many more details on my experience and is available here (MS Word document).

I am presently booked for Fall term 2006, but I am available for up to 20 hours per week after that. My rates are negotiable and what I get to learn on the project definitely counts. If the project involves developing a computational model of the behavior of microbes within biofilms, not only will I cut you a deal, I'll do a little happy dance. I can charge by the hour or by the project, whatever is best for you. If you're interested, I would be happy to offer a free one hour consultation to discuss your project.