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March, 2008: Volume 1, Issue 1

Welcome to the first issue of our newsletter, the Rosetta Biosoftware Messenger!

We develop each issue of Messenger with one goal in mind: to help you with your research.

Take advantage of our expertise.

The newsletter features voices of Rosetta Biosoftware employees and product managers. We’ll also feature the latest product developments we have to offer you, as well as real-world examples of how customers and researchers use our products. In addition, we’ll focus on a different product or event for each issue to give you timely, in-depth coverage of our products.

We hope you find our newsletter helpful.

 

Features of the Rosetta Resolver® system are highlighted as we prepare for the Society of Toxicology (SOT) annual meeting, which takes place in our hometown of Seattle, Washington.  Take our Survey (open in browser)

 

Cheers,
-The Rosetta Biosoftware Messenger Editorial Team

 

 

In this issue:

Product Update

You’re Only as Good as Your Annotation…
By Aubree Hoover, Product Manager, Rosetta Resolver System

It’s a message that I’ve heard from our customers time and time again, and one the Rosetta Resolver® team has taken close to our heart. We spent 2007 dedicating half our development team to streamlining gene annotation administration for our users and introducing functionality that allows our customers to do more in-depth cross species and cross technology studies than ever before! See the story on one customer’s ability to use custom array annotation to compare between two very different microarray technologies for more information.

 

At the same time, being the leader in gene annotation just isn’t enough to satisfy the Resolver system development team anymore. While half the team took on gene annotation, the remaining half took on the management of sample annotation data. Now users can load these data from spreadsheets quickly and automatically build experiment definitions based on these spreadsheets. This enhancement has resulted in a massive increase in productivity for many of our customers. See the application tip to see how this new version 7.1 feature can speed up your work (don’t worry, we won’t tell your boss).

 

These 7.1 features and others will be highlighted at this year’s Society of Toxicology meeting, which takes place from March 16th-20th in our hometown of Seattle, Washington. This year we will host a hospitality suite on the evening of March 17th where our Field Application Scientists and I will be on hand to demonstrate new features (while our guests enjoy some local wines). The following morning on March 18th at 8:30AM we will host a workshop highlighting some of the data integration and sample annotation work we’ve done in conjunction with the Predictive Safety Testing Consortium of the Critical Path Institute. Please see our conference page for details on all our events. I hope you’ll join us!

 

 

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Case Study

A Faster, Easier Way to Load and Use Sequence Annotation Data

The Sequence Annotation Engine in Resolver system version 7.1 provides a fast, automated, and transparent way to load and configure annotation data from databases such as GenBank, Gene Ontology Consortium, and Entrez Gene. In additon, the engine allows you to configure custom annotation data. In this article, we’ll show you how a Resolver system customer used the Sequence Annotation Engine and custom array annotations to make data comparisons between different microarray platforms.

 

When sequence annotation data (which can include descriptive text and accession codes for genes) are loaded into the Resolver system database, the Sequence Annotation Engine combines data from different sources in one simple step. The result is the generation of three types of annotation targets, which are “Sequence,” “Sequence Group,” and “Mapping” (Figure 1).

 

A Resolver system customer recently used Sequence Groups of custom array annotation data to compare two different microarray technologies. The presence of multiple array technologies and data formats can present several challenges when making comparisons across genes from different sources. For example, perhaps you need to compare data generated with older microarray technology to data generated with a new technology. When differences between array platforms are not accounted for, you can end up comparing apples to oranges.

 

Our customer wanted to compare data between two gene expression plaforms that used completely different biochemical processes to measure gene expression. In the past, the only solution was to compare these formats at the Entrez Gene-level. However, with the Resolver system version 7.1 and the Sequence Annotation Engine, the customer was able to determine which probes between the two platforms were truly comparable and load these data as “custom annotation” data into the Resolver system. This information was used to create Sequence Groups in the Resolver system, which linked a set of sequences in different array patterns for the same species (Figure 2). The same concept has been used by other customers to create “Mappings,” that link sequence groups for custom cross-species analyses.

 

Ultimately, the customer was able to use the custom annotation data to make the comparisons they needed. The Sequence Annotation Engine allowed their organization to use and compare years of legacy data generated on one microarray platform to data in the public domain, and newly-generated data on other array platforms.

 

Contact your Technical Account Manager today to determine how you can leverage the benefits of this faster, easier, and more transparent process for incorporating annotation data to enhance your research.

 

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Application Tip

Create Templates for Loading Clinical and Non-clinical Data

If you need to load or associate clinical and non-clinical data to an existing Experiment Definition, the Sample Annotation Text Loader is the tool for the job. To use this tool, you must be assigned the Sample Annotator or Lab Manager role in the Resolver system.

 

To save time, the Sample Annotation Text Loader allows you to create and use templates for loading data efficiently. You can also associate intensity or ratio experiments with existing Experiment Defintions or create a new Experiment Definition with Sample Annotation templates.

 

We’ll show you how to create a new template for loading clinical/non-clinical data files using the Sample Annotation Text Loader.

  1. Go to File > Import > Sample Annotation Text Loader to access a list of available templates.
  2. Select New Template to open the “Sample Annotation Import & Custom Fields Mapping Wizard.”
  3. Choose data files to import and configure column headings and delimiters.
  4. Specifiy the type of annotation data, or model, and map file columns to annotation attributes.
  5. Save your new template for future use.
  6. The next time you open Sample Annotation Text Loader, find your template file, locate the file(s) you want to load, and click Finish.

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Employee Highlight

Mette Peters, Ph.D., Research Fellow

Mette Peters joined Rosetta Biosoftware in 2004. She has played a valuable role in advancing scientific collaborations and research at Rosetta Biosoftware. This year, she will be presenting a poster at the Society of Toxicology (SOT) annual meeting. Her poster, “Temporal pattern of skeletal muscle gene expression following prolonged endurance exercise in Alaskan sled dogs,” can be viewed on March 17 from 1:00–4:30 PM at the Convention Center, Poster Board 234.

 

Mette took the time to explain the research behind her poster and discuss her favorite aspects about working at Rosetta Biosoftware.

 

What was the goal of the study?

The goal of the study was to better understand the temporal responses in skeletal muscle gene expression after exercise to examine short term energy need and long term adaptation responses.

 

How did you use the Resolver system for this particular study?

The Resolver system was used for all the data processing and profiling analysis in this study.  The Resolver system has a comprehensive list of analysis and visualization tools; our study just scratched the surface of what the Resolver system can do.

 

Can you tell us about your educational background?

I hold a Ph.D. in Cell and Molecular Biology from Purdue University, and was a Postdoctoral Research Fellow at the Fred Hutchinson Cancer Research Center working on a large collaborative project screening high-risk families for prostate cancer susceptibility genes. Prior to joining Rosetta, I managed the microarray core facility at the University of Washington.

 

What do you enjoy most about working at Rosetta Biosoftware?

Rosetta Biosoftware is a company with a great mix of people from different professions.  Being able to work with people ranging from Developers to Sales Associates provides a very stimulating work environment. And, what is truly enjoyable, is of course being able to promote analysis tools that can truly provide scientific solutions.

 

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Materials

Webinar Available for Download:

Validation of Peptide Assignments to
MS/MS Spectra and Inference of
Proteins Using the Elucidator System

Presented by: Andrew Keller, Ph.D.,
Research Fellow, Rosetta Biosoftware

Date: January 23, 2008

Summary: This Webinar describes
PeptideTeller™ and ProteinTeller™
functionality to facilitate protein
identification, now present in the Rosetta
Elucidator system version 3.1.

Click here to log in and download this Webinar.

Case Study Available for Download:

Application of the Rosetta Syllego
System in Genetic Data Management
and Analysis

Summary: This case study uses publicly
available genotype and gene expression
data and the Rosetta Syllego system to
identify significant associations between
genetic markers (SNPs) and baseline
gene expression profiles in a defined
population.

Click here to log in and download a copy.

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Events

Rosetta Biosoftware 2008 Conference List

Mark these dates on your calendar to visit Rosetta Biosoftware at the following conferences:

Resolver System
3/17/08 - 3/19/08
Society of Toxicology (SOT) Annual Meeting,
Seattle, Washington, USA

Resolver System
4/12/08 - 4/16/08
American Association for Cancer Research (AACR) Annual Meeting,
San Diego, California, USA

Syllego System
4/17/08
Illumina® User Group Meeting at AACR Annual Meeting,
San Diego, California, USA

Elucidator System
6/1/08 - 6/5/08
American Society for Mass Spectrometry (ASMS),
Denver, Colorado, USA

Syllego System
11/12/08 - 11/15/08
American Society of Human Genetics (ASHG),
Philadelphia, Pennsylvania, USA

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