Monday, January 21, 2008

Google will help on scientific data management

In biology/medicine, there are lots of data need to well annotated rather than only providing storage. It would be better if Google could integration it with semantic web technology.

In bioinformatics field, there are many emerging new database to collect data set or molecules annotation , i.e. database on DNA methylation, microRNAs etc. At least, we can publish a new database using Google Base right now. We can avoid waster time on writing code for search and user interface using the search engine of GOOGLE BASE.

Google's Palimpsest project: promiscuous distribution of all science data sets

Friday, January 18, 2008

What is a good biomarker?

  • represent distinct phenotype
  • rich mechanisms related information - especially in the stage of in silico prediction/identification stage - NO biologists will happy to or have the instant capability to validate a poor-mechanisms related biomarker
  • ROBUST - robust across different data set, measurement platform
  • applicable and economic is also key factor of fast translational the candidate biomarker to real word application
  • ...

Oncomirs - microRNAs with a role in cancer

Its glad to see the term "Oncomirs" appear in a formal publication:

microRNAs could labeled by "oncogene like microRNAs" or "tumor suppressor genes like microRNAs" according to their action on cancer.

I suggests "OncoRNA" cause there may another type of regulatory RNAs could also be labeled based on their positive or negative action on cancer development.

Thursday, January 17, 2008

coding information of DNA methylation and microRNAs

epigenetic coding - stable
microRNAs information - median stable
gene expression - sensitive to environment stimulus, variable

information flow

What should we found the hidden value of a published paper?

what 's the hidden value of a published paper ?
  • philosophy - the author may not express more on their preferences, understandings, cause any sententences should be reasonable - its a basic demand of solid publication. Thus we need relies on ourselves to extract the initial understandings/ideas of authors
  • testbed - a testbed is a collection of resources, the input/output, how to validate it and claims sth. based on it.
Why philosophy is important?
  • it is abstraction layer, which could direct novel knowledge discovery
  • the application of philosophy can lead to new new results on different situations
  • for example, each new algorithm in Machine Learning could be based on the philosophy