nodalpoint.org - Forum topic - Comments

How is bioinformatics influencing stem cell projects?

chris — Fri, 18 Apr 2008 12:43:33 -0400

Perhaps you can tell us how, in your mind, bioinformatics is speeding up stem cells projects. Then we can go from there...

It's probably a bit late, but...

gpjt — Wed, 05 Mar 2008 07:35:32 -0500

Greg,

It looks like my colleague Jean missed your question - sorry for that!

Resolver One is now at version 1.0.1, and it's free for non-commercial use. For regular commercial use (online support in our forums, etc) it's $199 (reduced to $99 until the end of this month), and there is also a financial version with market data feeds, telephone support, SLAs, etc, on a rental model.

There's also a web server, which can serve up your spreadsheets as simple web applications - this is $699 (currently reduced to $499) per server machine, no client licenses required.

Regards,

Giles

R objects, and contacting authors

chris — Thu, 24 Jan 2008 10:27:34 -0500

I seem to recall that the limma/rma packages also have an option to return R and G values. Otherwise you can back-calculate from M and A.

M = log2(R) - log2(G)
A = 0.5*[log2(R)+log2(G)]

If only normalized data is available online, your best bet is to contact the authors and ask for raw intensities - there is no way of recovering them from processed data (at least, I don't think so).

They're cDNA data, according

lbbros — Thu, 24 Jan 2008 06:27:01 -0500

They're cDNA data, according to the paper (Zhao H et al., PloS Medicine 2005).

To tell you the truth, I'm not sure at all about consistency - but it's like a "test run" for a completely different approach I'm using: I'm just trying to see if such an approach is even feasible for the algorithm I'm going to run over the normalized data.

cDNA or oligo data ? Are you

Greg — Wed, 23 Jan 2008 11:42:14 -0500

cDNA or oligo data ? Are you sure the consistency of the data is good enough to be doing single channel normalization ?

bioinformatics code? ok..

dalloliogm — Sun, 11 Nov 2007 11:22:10 -0500

bioinformatics code?
ok.. let me think a while about what I can upload.

In the meanwhile, this is my favorite code from that site:
- http://refactormycode.com/codes/51-classtemplate
it is a template for a class in python, showing how to use the pydoc and dontest modules, which I didn't know how to use properly before.

Refactor Bioinformatics

Duncan — Fri, 09 Nov 2007 07:44:18 -0500

looks interesting. You could try uploading some bioinformatics code to their site and see what feedback you get?

forum posts?

dalloliogm — Fri, 19 Oct 2007 09:54:35 -0400

Well.. and what about referencing forum posts in a thesis/article?

Examples of good forums on biology/bioinformatics:
- http://www.protocol-online.org/forums/index.php
- http://molecularbiology.forums.biotechniques.com/forums/index.php
- http://www.biology-online.org/biology-forum/
- http://nodalpoint.org/forum
- http://www.molecularlab.it/forum/

Blog citation index

Neil — Fri, 19 Oct 2007 00:00:03 -0400

The NCBI now have guidelines for citing blogs

That's cool! Now all we need is a way to record when someone cites our blog, then we can build the blog citation index ;)
Oh wait, this is the brave new world, not an attempt to mimic the old one.

NCBI guidelines

alf — Wed, 17 Oct 2007 10:41:04 -0400

The NCBI now have guidelines for citing blogs.

This is a very intriguing

Greg — Sun, 14 Oct 2007 21:48:21 -0400

This is a very intriguing application, and I can see why you've posted it here. Could you provide some more details on product licensing ?

OneNote alternative

glh — Fri, 12 Oct 2007 15:04:31 -0400

A OneNote alternative that I've seen mentioned is a Java application called Memoranda: http://memoranda.sourceforge.net/overview.html

I haven't tried it personally so I don't know how well it works but it does look interesting. It gives you a place to create notes as well as track tasks, meetings and resources (links to related files). Everything appears to be organized by projects, which may or may not work for your needs.

Interesting, but...

lbbros — Thu, 11 Oct 2007 17:51:58 -0400

It is definitely interesting, however not applicable to my case as I have stopped using Microsoft's OS since two years ago. The other post about ELN looks interesting as well, and I'll give it a try if I can.

From the posting guide...

chris — Thu, 11 Oct 2007 15:45:21 -0400

See here:

Be nice, be interesting. You'll find we are, mostly. Try to keep it brief. See our resources page. Sorry, we don't do homework.

Microsoft OneNote 2007

glh — Thu, 11 Oct 2007 11:53:24 -0400

The latest version of OneNote has the capability to organize notes into notebooks with some of the capabilities of a wiki. OneNote is an electronic notebook that you can organize into notebooks, sections and pages in whatever way works best for you. With the latest version notebooks can be shared on a network, but a local copy is cached to your hard drive. If you connect with a laptop you can work offline and when you connect to the network again the two versions are automatically merged (unless you specify otherwise). Editing by multiple users is also supported. Links can be made between information on multiple pages so you can navigate between related information in much the same way you do in wiki. They have also added some very nice integration with Outlook (2003 or later) that provides the ability to create links from meetings, tasks and emails that link to the related notes in your OneNote notebook. Outlook tasks and meetings can also be created directly from OneNote.

OneNote also has a built in print driver that can be used to "print" documents such as PDF files directly to to OneNote. By default text is extracted from images using the built in OCR capabilities to make these searchable. Here is an example from another blog of someone that uses this for keeping track of journal articles: http://missionarygeek.blogspot.com/2007/07/using-onenote-for-academic-jo....

OneNote pages can also have freehand notes written on them using a mouse if you're on a regular PC, or with a stylus if you are using a tablet PC. This way you can add comments or highlight text on PDF files, presentations or other documents imported into OneNote without worrying about reformatting the original document. The ideal situation is to have a small tablet PC that you can take with you everywhere so you always have your notes with you and you can add new notes, although I haven't had a chance to try this yet. Most of the features mentioned require OneNote 2007 and Outlook 2003 or later.