Tag Archives: resources

“What’s the Answer”

BioStar is a site for asking, answering and discussing bioinformatics question

s. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Today’s question and answer is:

Recommend easy to use microarray clustering software

The most highly voted answer (was the author who posted the recommendation thread):

One of my favorites is the MEV micro-array data analysis tool. It is simple to use and it has a very large number of features.

Works well for any type of data. You can also load into it data from a file that is in a simple text format:

GENE1, value1, value2
GENE2, value1, value2

Feel free to post your favorite clustering tool.

Several other excellent tools were suggested, you can check them out here.

Real bioinformaticians write code, real scientists…

Just over a week ago, Neil Saunders wrote a post I agreed with: Real bioinformaticians write code. The post was in response to a tweet conversation that started:

Many #biostar questions begin “I am looking for a resource..”. The answer is often that you need to code a solution using the data you have.

He’s right, and that’s very true for bioinformaticists to whom he’s talking. My concern is for the rest of biological researchers. He states in the post:

In other words: know the data sources, know the right tools and you can always sculpt a solution for your own situation.

This is very true and I whole heartedly agree. So many solutions exist already in thousands of databases and analysis tools. It’s what we do here at OpenHelix, help experimental biologists, genomics researchers and bioinformaticists find the right data sources and tools and then go and “sculpt a solution for their situation.”

In the last part of my comment,

BioMart, UCSC Genome Browser, Galaxy, etc, etc are excellent tools and data sources and could probably answer about 80% of most posed questions :). But my caveat would be that knowing the data sources and right tools can be a bit of a daunting task.

And it is, despite the somewhat dismissive response :). We’ve all seen the graphs, exponentially rising amounts of data over time. It’s an issue as the Chronicle of Higher Education article title states:

Dumped on by Data: Scientists Say a Deluge is Drowning Research

The journal Science also had an entire 10 article section on the issue. It’s not a problem that will go away.

Along with that deluge of data, has come a deluge of databases and data analysis tools (created for the most part by bioinformaticists!), many of which _alone_ are quite daunting to find the right data and tool within. There are thousands such databases and tools. I’ve lost count.

Neil Saunders is correct. The solution is out there, find the right tools and data, sculpt a solution. He responds to my comment with “Learning what you need to know in bioinformatics can certainly be daunting. But then, science isn’t for for the easily daunted :-).” In other words, “if you are daunted, you aren’t a scientist?”

We give workshops to researchers around the world from Singapore to the US to Morocco and at institutions as varied as Harvard, Stanford, University of Missouri, Mt. Sinai, Stowers and Hudson-Alpha. The researchers we’ve given workshops and answered questions from were also varied, developmental biologists, evolutionary, medical researchers, bioinformaticists, researchers quite well versed in genomics and those not.

The overriding theme is finding and knowing the data and the tools is not only daunting, but sometimes not possible. Not because they don’t exist, but because finding and knowing them is a drain of personal and lab resources considering the shear growing field of things to find and know. I refer you to the Chronicle article… drowning in data..

They are real scientists not easily daunted, but daunted just the same, by what’s in front of them. And yes, many of those specific questions to specific research needs can be answered by existing tools. We come across many questions on Biostar that a well-crafted database search or analysis step will answer beautifully, without the need for reinventing the wheel with more code (and the answers are often code).

I suspect that most of those scientists out there who call themselves ‘bioinformaticists” should have a grasp of the tools and databases available to them (but I can tell you, even the brightest of them don’t sometimes). So, the advice and final words of the linked blog post above…

In other words: know the data sources, know the right tools and you can always sculpt a solution for your own situation…. real bioinformaticists write code

Yes, real bioinformaticists write code, but this advice is insufficient to the other 90% of real scientists who don’t. Perhaps Biostar is not the solution (I suspect a lot of those questions being asked he points out are those by non-bioinformaticists who only have a basic, if any, knowledge of coding nor access to those who do). Perhaps it, or something like it, can be.

Tip of the Week: Finding the right genomics resource

ohsearch_thumbOpenHelix just opened our new web site. We will still be offering the tutorials we’ve always offered (80 and growing!), but now we have a new search engine and database of many more resources. And it’s publicly available and free.

There are now thousands of databases and analysis tools for the researcher to use when doing research in biology and genomics. The first problem the researcher has is just finding those resources, finding the right one. In another step toward helping that happen, we’ve put together a highly relevant, curated database of genomics and biological resources available to the researcher and a search engine to find them based the context of the keyword found at the resource site, tutorials and even our blogs posts that mention the database. You will find that your searches will lead you to resources relevant to your needs. Today’s tip introduces this new search.

We strongly believe this is the best method available now for the researcher not only to find relevant resources, but to find training on how to use those resources. And check back, our database of resources will be growing, as will our features.