Hot Bioinformatics

Personal Genome Project - United Kingdom ... well not quite!

2014-05-21T13:18:00.001+01:00

What is going on at the Personal Genome Project UK ?

So, the Personal Genome Project has been in hot water recently because of the huge privacy blunder they did by releasing participants names in the mailing list which they have now issued a public apology for... (http://personalgenomes.org/uk/email-storm-incident-and-apology).

But despite the trepidation I still though I would like to participate and after a huge convoluted application process I finally got registered.... Hurray!

However, someone needs to take the reigns on this thing and put it in the right track soon because it currently is a train-wreck!

Here is why:

After I got registered I decided to fill in my profile and contribute my medical data. I believe only if the participants are wiling to share this type of information will a huge sequencing project like this be able to succeed in bringing about new discoveries... but the webpage is simply unusable. Someone just copied the Harvard study codebase (http://www.personalgenomes.org/harvard) and so the page for a UK based study, funded by the UK taxpayer is completely unusable by UK citizens!!!!

WTF!!!!!!

1) The Personal health records page fails to import your personal health record file

They claim to support the import of CCR files (Continuity of Care Record files) and they even describe how you can use Microsoft HealthVault to add your information and produce the required file to submit to them... However when you go though the trouble of doing so...

here is the message you get:

2) All forms requiring addresses are in the United States!

This one is particularly damming! For a UK based study, paid for by the UK taxpayer you cannot add your address information to you profile, or indicate your geographical origin because all forms require you to add the US state... don't believe me ...look at the screenshot:

3) Impossible surveys:

They request you to fill in 2 surveys: Geographical information and Absolute Pitch Survey but the first one requires you to select a US state, and the second one ... well this happens:

For such a high profile project, they will be spending millions doing sequencing ... I am certain they could send a tiny bit of that money making a website that has some minimal functionality!

All of what I am detailing in this blog post has been submitted to them by their contact email... but you guessed it ... it is not working!

If they are as careless with our data as they are being with the development of their website we are all in deep trouble!

Why are Genome Browsers Stuck on Web1.0??

2012-08-29T17:18:00.000+01:00

I was wondering when will we see the latest advances in javascript performance, local storage APIs and improvements in the HTML5 standards start to make in impact on the main online genome browsers out there?

http://www.ncbi.nlm.nih.gov/mapview
http://genome.ucsc.edu
http://www.ensembl.org/index.html

I use UCSC genome browser more than the other two because of the great customization and collaboration features they provide, but like the others ... these websites are still stuck in the last century when it comes to web technologies!

Could you image a USCS genome browser with pan and dynamic zoom capabilities similar to Google maps, With annotations tracks that adjust dynamically to the level of zoom and show only the appropriate level of details? Couple that with great collaboration features and easy import of custom annotation tracks (drag and drop files similar to what you can do with gmail attachments interface) and you would have an amazingly powerful platform.

#genomebrowsers #genomicresearch #web20 #ajax #ngs #nextgenerationsequencing

Interview

2011-03-21T15:54:00.003+00:00

Well it seems by small blog has some following because I got an interview about it :)

It was a few month ago but I completely forgot to post it

Interviste Duarte Molha dell OGT

Hope you like it.

Duarte

Craig Venter on TED

2010-05-27T10:47:00.001+01:00

It is a somewhat older talk from 2008 but very relevant to the latest news that they have successfully created the first syntetic lifeform

Juan Enriquez does to TED once more

2009-02-23T10:11:00.001+00:00

Once again Juan Enriquez gives a tremendous presentation of some of the problems facing us and some of the extraordinary research being developed to takes to a brighter future... a worth 30 minutes of knowledge into what he calls the ultimate reboot of human technology and the emergence of Homo evolutis

Genomic Revolution

2008-02-20T00:40:00.001+00:00

All you need to know about Microarrays

2007-07-03T18:52:00.001+01:00

BioSolutions: DNA Microarray

DNA Microarray
Nice post with videos about microarray technology

Nuclear fusion breakthrough!!!

2007-06-27T00:44:00.001+01:00

Should Google Go Nuclear? Clean, cheap, nuclear power (no, really)

Poor quality slides but the content is really revolutionary.

I hope this really is true! It will end our dependency on oil!!!!

Harvard, Princeton researchers developing implantable "biocomputers"

2007-05-21T22:59:00.001+01:00

There you go... The future is coming sooner than you think
Harvard, Princeton researchers developing implantable "biocomputers" - Engadget

Harvard, Princeton researchers developing implantable "biocomputers"
Posted May 21st 2007 5:11PM by Donald Melanson
Filed under: Misc. Gadgets
Researchers at Harvard and Princeton have announced that they've made a "crucial step" in the development of so-called "biocomputers," which could one day be implanted in patients to directly attack diseased cells or tissues Fantastic Voyage-style. According to Physorg, the computers are actually constructed entirely out of DNA, RNA, and proteins, and are able to translate complex cellular signatures like the activities of multiple genes into a form that can be more readily observed. Currently, the researchers have demonstrated that the biocomputers can work in human kidney cells in culture, although they seem confident that they'll eventually find a wind range of uses, including working in conjunction with biosensors or medicine delivery systems to target, for instance, only cancerous or diseased cells, without causing any harm to the patient's healthy cells.

NCBi redesign their Blast Inferface

2007-04-26T12:02:00.001+01:00

If you go to NCBi you will find that they have improved their Blast Interface
Personally I think that this was long overdue :)
Check it out !
http://www.ncbi.nlm.nih.gov/blast/

Duarte

Bio-linux on Ubuntu

2007-04-05T03:00:00.001+01:00

UPDATE:
Seems like to website with these instructions went offline. For those still interested you can find the instructions on the wayback machine on the following link:
http://web.archive.org/web/20060623041126/hocuspok.us/tag/ubuntu/
Hope you find it usefull

Duarte

Great tutorial on how to install and extensive collection of Bioinformatics tools for Ubuntu

hocuspok.us: Bio-Linux - Bioinformatics Tools for Linux

Hello World!

2006-10-14T15:53:00.000+01:00

Hello everyone! Welcome to my blog
I've set this blog to keep in track of the hottest news about my field of study - Bioinformatics
I think it is a great way of organising information you find usefull and hopefully I might help other as well.

Cheers,
Duarte Molha