Yes, it was. I attest to that statement with [quite] a few publications for evidence.

"Biologists know their pathways" is a dangerous proposition. First, it's not about them, biologists and us, presumably something else. One can't handle an advanced tool effectively without being a biologists. Second, some researchers tend to focus on a single gene, single hypothesis, single pathway, which may or may not turn out essential. This focal approach is common recipe to successfully complete the study, make a publication and miss the discovery. It can be balanced by a broader view provided by those expensive advanced tools with all conveniences, bells and whistles. You don't need this unless you are going to spend hours clicking around trying to figure out the way things happen in the experiment, the meaning of expression level changing in all directions and patterns in chaotic shadows. Simple things like grabbing some Cytoscape, routine GO tables and enrichment tests are perfect if you do your job 9 to 5, perform your duties of highly qualified specialist and let them clients, biologists, doctors worry about discoveries. This is how core facilities usually operate. I concord with your point, all those "advanced" tools are not as advanced under the hood as one may think reading their sales booklets. They also don't solve the problems and make discoveries. However, these fancy tools give you a better fighting chance if you know how to use them.

Yes, it was. I attest to that statement with [quite] a few publications for evidence.

"Biologists know their pathways" is a dangerous proposition. First, it's not about them, biologists and us, presumably something else. One can't handle an advanced tool effectively without being a biologists. Second, some researchers tend to focus on a single gene, single hypothesis, single pathway, which may or may not turn out essential. This focal approach is common recipe to successfully complete the study, make a publication and miss the discovery. It can be balanced by a broader view provided by those expensive advanced tools with all conveniences, bells and whistles. You don't need this unless you are going to spend hours clicking around trying to figure out the way things happen in the experiment, the meaning of expression level changing in all directions and patterns in chaotic shadows. Simple things like grabbing some Cytoscape, routine GO tables and enrichment tests are perfect if you do your job 9 to 5, perform your duties of highly qualified specialist and let them clients, biologists, doctors worry about discoveries. This is how core facilities usually operate. I concord with your point, all those "advanced" tools are not as advanced under the hood as one may think reading their sales booklets. They also don't solve the problems and make discoveries. However, these fancy tools give you a better fighting chance if you know how to use them.

Dear Andrey,

Thank you for this detailed answer, and happy New Year !

I would indeed be interested to see the publications you are referring to.

However I am curious how they relate to your last statement:

>

Especially in the context of your agreements that these are merely nicer looking tools.

Were any of those advanced tools significantly instrumental in the discovery?

Concerning my statement that "biologist know their pathways", I was deliberately provocative here. I firmly believe that brillant scientists, whether they are Biologist, Bioinformatician, Clinician, etc., can learn/understand any related fields, but are better off as expert in their own field knowingly discussing with experts in those neighbouring fields. However, I realise this discussion might require its own topic...

Best wishes

Jean-Baptiste

This kind of tool is also a good start up for research.

I know it's a provocation, but happy to oblige.

The tools don't make discoveries - you do. A good tool in Computational Biology is not merely nicer looking. It's powerful and ergonomic. It might be doing the same thing as a script you fix in vi and launch in command line, but it could (not necessarily will) give you a better shot at discovery. Allegorically speaking, you can hummer a nail with a rock, but if you have a house to keep it might worth to consider buying a hammer, maybe even with a shiny head and ergonomic handle. A nail gun does essentially the same thing you can do with a rock and a nail, but it may bring your productivity to a new level.

Dear Narcis,

I appreciate it can be an easy way to summarize existing knowledge on a new project. However with a limited number of new project requiring such boot start, it can be an expensive way, especially with cheaper, simpler, solutions.

Dear Andrey,

I agree.

Hence my interest on those articles you have been referring to.

Thanks

Yebo, expensive they are and I used to be grumpy about that too. However, I was lucky to convince the employer to pay for it. A single concurrent login is a drop in a bucket even for a small university, particularly with multi-year license discount. Looking back I'd say it was worth every penny.

Most of my publications are in open access domain, you can use my profile to download. Here's the shortlist:

Resveratrol suppresses human colon cancer cell proliferation and induces apoptosis via targeting the pentose phosphate and the talin-FAK signaling pathways-A proteomic approach.

Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment.

Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome

Computational analysis of gene expression space associated with metastatic cancer.

Persistent fetal infection with bovine viral diarrhea virus deferentially affects maternal blood cell signal transduction pathways.

Systems biology approach to identification of biomarkers for metastatic progression in cancer

Unsupervised clustering of gene expression data points at hypoxia as possible trigger for metabolic syndrome.

Thanks Andrey,

I shall have a look

I hope this would be useful to others.

PathwayTools (http://bioinformatics.ai.sri.com/ptools/) is also great to work with pathways, lots of features and possibilities to query the pathway/graph

"A good tool in Computational Biology is not merely nicer looking. It's powerful and ergonomic."

I kind of disagree here. First, being powerful and ergonomic should not prevent the tool being pleasant for the eye (and vice-versa). Second, powerful and ergonomic are very subjective and totally depends and what you try to achieve. For example, would you rather use Photoshop or ImageJ to analyze microscopy images? ImageJ is probably a better choice, even though in general, PS is more powerful, more ergonomic and better looking...

We are a long ways from clinical-grade pathways analysis...see my recent question, which was from an article using a very highly regarded pathway analysis system (IPA). 

People sometimes try several different pathways analysis and then cherry-pick those findings that have biologic relevance to the genes/proteins they are examining. 

Part of the problem is that, with the deluge of publications, it is phenomenally expensive to keep pathways updated. Also, it is not always clear which species, or which cells, or which developmental stage the pathway analysis was derived from. This is a particularly difficult problem for clinical CNS disease. No easy answers!