Diving into standard protocols – First thoughts

To begin with, I want to present a simple approach to construct a XML based structure for biological protocols: To those of you that don’t know what XML is, you can refer to http://en.wikipedia.org/wiki/XML.

As I believe, based on my experience with several known molecular biology protocols, We can break almost every protocol to several different elements that can be thoroughly defined with standard properties.

I won’t show the elements type and properties I thought of yet, but instead show the general, abstract protocol structure.

The main structure of biological protocols:

<protocol>
      <element type=”…”/>
      <element type=”…”/>
      <element type=”…”/>
  …
</protocol>

Since every protocol have some “meta-data” like author, date, description etc. , I think the best thing will be to present this data in the header of the protocol:

for Example:

<protocol   name = “The protocol name”
                   Author =”Author name”
                   source =”…”>
    <element type=”…”/>
    <element type=”…”/>
    <element type=”…”/>
  …
</protocol>
 

And finally each element should include some properties that describe that describe the properties of the action done in the particular method’s element like:

<protocol   name= “The protocol name”
                   Author =”Author name”
                   source =”…”>
    <element type=”…”>
            <property type=”…”>
                   …property of the current element…
            </property>

    </element>
    <element type=”…”/>
  …
</protocol>

 

 This hierarchical structure will allow the computer a lot of freedom in understanding protocols:

1. The software will be able to decide what is the function of each protocol’s part and element: if it is a title, a description, a remark or action.
2. The computer can draw the relationship between different parts of the protocol.
3. Different protocols can be compared according to their structure and order, even without understanding the meaning of the words.
4. It is very easy to present this protocols according the the user preferences, in a way that every protocol is presented with the user recognizable template, a fact that can ease the way he can understand the protocol, and shorten the learning curve.

 

In the next posts, I get more deeply into this scheme and show some simple protocols that obey these standards, and the methods to present it.

Later on. I’ll keep building a small database of standard protocols and while doing so, I’ll try to develop my standards even more.

 

Why to use standard biological protocols?

Welcome to the new standard biological protocols website. This site will focus mainly on constructing new standards for writing, viewing and deploying biological protocols.

You are probably asking what standards I am talking about and what exactly my agenda is.Well, as a biologist I find myself over and over again chasing and learning new lab methods every day, currently there is a large literature pile of countless protocols coming from many different origins like articles, books, technical papers, companies’ brochures and manuals.

The facts are that although the protocols are out there and are easy to reach, they are written in a very diverse ways and so, the case is that with every new protocol you find, you need to struggle all over again with the writing and the terminology, and often, just understanding the protocol’s structure takes a long time.

Constructing a new standard to write and present biological procedures will provide the best solution to rapidly understand new protocols which are written in a familiar way, and use a known convention.

In addition, the best place to put protocols today must be online. The internet has become the number 1 information resource available, and the most prominent way by which people, including scientists, search for information. As such, making biological protocols more standard will ease the way computer algorithms can search and sort biological methods, and make the search for known methods much easier and efficient.

Making these methods more understandable to computers will lead to more sophisticated seeking practices that can save a lot of time, picking the right procedure to the right task. Moreover, by making bio protocols accessible to computer software, we can open a new research horizons for bioinformatics scientists and system biologists that would be able to build new algorithms that can compare different experiments, by analyzing the experimental procedure, and the results.  Making so, will aid the currently deep problem of data mining of articles which looks impossible at present.  

Finally, as biological protocols become more and more standard and largely used by everyone, making them more standardized will offer a way to automate these procedure easily, and aid to replace the laborious daily tasks with robots, that will free the time to the researchers to  invest in learning and thinking and not with repeating the same procedure over and over again.

In the next posts I’ll start to discuss in details how do I think that protocol standards should look like, and start building examples of well known procedures. I’ll be glad to any comment about my protocols, and ways to improve them. I planning to built a new application to standardize protocols in the future. 

Dror.