Creating Connections in WayFarer

March 27, 2008

In our previous screencast we demonstrated how to create biological entities and how to represent variations in those entities using standard nomemclature. We’ve just completed a screencast that demonstrates how to connect those entities via biological interactions. This is an important step in the description of our systems biology tool, we are now showing how the user can connect the dots.

For a larger view: http://www.waycraftbio.com/PathwaySteps.html.


Doodling for Profits

March 3, 2008

A recent article in Business Week touts the wonders of doodling, or drawing simple sketches, to get a point across. This really comes as no surprise to us at WayCraft, we’ve always believed in the power of diagrams to illustrate an idea. Unfortunately there are two problems with doodling on cocktail napkins:

  1. It doesn’t scale
  2. They don’t store very well

Diagrams on white boards or cocktail napkins are great for brainstorming sessions but taking those high level ideas to the next level may require four or five white boards, or a stack of cocktail napkins, worth of information. The ideas must be transferred to a more expandable medium pretty quickly after the original session.

Transferred to what is the question. Word documents, Excel spreadsheets, Powerpoint presentations are the most common forms of capturing these ideas. What was once a simple and powerful diagram has quickly become just another document or presentation. Microsoft Visio offers a host of standardized, pre-drawn images but that’s where it ends; images without significant meaning.

WayFarer provides the power and simplicity of graphical representation along with the ability to annotate the drawings with much more meaning. These drawings can then be organized and stored on your computer for later retrieval and transfer to other users.


WayFarer Variant Wizard

February 28, 2008

WayFarer now has a feature that allows a user to annotate molecular entities with genetic and molecular variations using standard nomenclature. These variants not only inherit the properties of their base entities but retain their association with the base entity as well.

For a larger display: http://www.waycraftbio.com/VWizard.html.


New WayFarer Screencast

February 27, 2008

In keeping with our policy of simplifying and streamlining knowledge transfer, we here at WayCraft are using screencasting technology to demonstrate the features of WayFarer. Our first screencast demonstrates WayFarer’s ability to integrate external data sources within its user interface.

A larger version of this screencast can be viewed here.


Negative Results

January 30, 2008

Although scientists are trained to be objective about the results of their experiments, one cannot help being a bit more excited when the results are “positive,” i.e. the reaction occurred as you had predicted. This is cause for celebration, tell your boss and start writing your Nobel acceptance speech. At the very least the results will be written up and perhaps published.

But, as is often the case, the results do not always support the hypothesis. This is simply the scientific process; the results are written in a lab notebook, the hypothesis is revised and another experiment is performed to test the new hypothesis.

But what happens to the negative results? Yes they are written in the notebook and become part of the researcher’s knowledge which leads him to reformulate a new hypothesis, but are they captured in way which enables them to become part of the lab group’s knowledge base? Not in most cases.

WayFarer now has a feature that allows the researcher to capture this negative result explicitly and allow it to be easily shared with team or community members. Any reaction that can be asserted can be refuted as well. Refuting a reaction does not erase the reaction; rather it becomes the latest part of the reaction’s history. Refuting a reaction can also be done on a reaction that had been attributed to another researcher but had since been disproved or refined to the point where the previous results had to be restated.

By retaining this knowledge in an easily retrievable form, recounting the logical reasoning that went into developing a subsequent hypothesis and transferring that knowledge to another researcher will proceed much quicker with less effort. This allows you to leverage all of the results of your lab’s work, not just a highly filtered selection.


WayCraft Biosoftware Blog

January 22, 2008

The next time you have a two inch thick stack of articles that you have to read through by the next morning think to yourself; wouldn’t you rather have this represented on four or five easily interpretable screen displays? There finally is a better way of representing dense biological information and it will make all biologists’ lives a little easier.

WayCraft Biosoftware came into existence about two years ago, hatched from an idea Frank had been thinking over for some years; provide biologists with a system that could better represent and communicate their ideas and knowledge. The de facto tools for this are Microsoft Word and PowerPoint, tools every scientist uses but provide very little in the way of any scientific framework.

On the other end of the spectrum are biological simulators; computer models that have been developed to simulate biological systems and replace the need for live animal or human subjects. Most biologist don’t use these in their everyday work flow, they are at present in the realm of advanced research departments.

WayCraft’s platform, WayFarer, is a software product designed for the bench biologist, an environment where they can aggregate their piles of pdf’s, capture their ideas, design their next experiment and share their results with colleagues. And because of the intuitive, graphic user interface, they can learn how to use it in hours.

Although each biologist has their own workflow we have attempted to capture those elements of the workflow that are common in all labs. We aren’t replacing the wet lab; instead we are making it work more efficiently.

Both founders of WayCraft, Frank Russo and me, Steve Connolly, have been writing our own blogs (Modelhead and Mind to Market respectively) but we felt it was time that WayCraft deserved a blog of its own in order to focus exclusively its unique and exciting products.