nodalpoint.org - Genetics - Comments

announcement vs. advertisement

yogibear — Thu, 27 Apr 2006 18:09:34 -0400

I have enquired in the irc #nodalpoint channel before posting, and Neil Saunders was kind enough to get back to me and enourage me to post. Announcements, by definition, are made by the people who have developed the product, aren't they? So yes, announcements are a special form of advertisement, and yes, I am from Biomatters. However, in this case the advertisement is for a freeware product.

I have never claimed that Geneious is open source. It is freeware, but closed source. We control the platform only in so far as we are the only ones who can make new platform releases. We can not take the existing platform, which we have provided for free, back from the community.

So the community will always be free to use that platform, and to develop plugins that extend the existing freeware version of the platform. I think it should be obvious that the community benefits from this possibility. What if the Eclipse platform was freeware closed source? People could still use Eclipse productively, and develop as many plugins as they feel like.

I personally think you should really reserve your aggressions for people who try to get your money, not for people who have just given you free stuff.

Please post announcements in

Greg — Thu, 27 Apr 2006 10:03:06 -0400

Please post announcements in the forums. Also if you are from Biomatters then this is not just an announcement it is advertising, in which case please let us know. For the moment I'll give this post published status, however not to the front page.

Also, I'm curious about Biomatter's claims regarding open source. The product itself is not open source, it only provides a plug-in API ? So that means you control the platform, in which case how does the benefit the community ?

writing style

chris — Fri, 23 Dec 2005 13:25:37 -0500

I'm a big fan of these sorts of articles. The best writing usually tells a story: a continuous narrative for some reason resonates deeply with the human mind and allows us to absorb information and place things into perspective. It's an old trick, going back to the legends and parables of the ancient worlds of Gilgamesh and Homer.

One of the things we often miss when reading/writing a scientific paper is this narrative: the introduction should at least set the scene, but in truth so many scientists are so poor at writing that their papers become garbled and abstruse, even for other experts in their field.

Maybe we should all try to tell stories in our next papers?

iHOP - Information Hyperlinked over Proteins

Robert Hoffmann — Sun, 09 Oct 2005 14:31:34 -0400

Thanks for that nice feedback!

I would like to inform you that the iHOP address has just changed to: iHOP - Information Hyperlinked over Proteins, www.ihop-net.org/UniPub/iHOP/

Best wishes,

Robert

RE: iHOP

Anonymous — Tue, 01 Feb 2005 21:29:45 -0500

To be honest, I like the highlighted text output better. It gives a nice grasp of the subtleties and complexities that often elude graphical depictions. If you're an iHOP person, great job!

RE: iHOP

Anonymous — Tue, 01 Feb 2005 04:40:12 -0500

Did you try this function for collecting sentences and building a graphical representation?! That's really useful to make a review about a gene or something (iHOP).

Usability

Greg — Wed, 28 Apr 2004 09:28:21 -0400

Maybe its just me but I find the usability of the majority of online bioinformatics databases to be really poor. The JBIRC database, I'm sure is very comprehensive and technically brilliant but suffers from usability problems (admittedly my usability testing consists of see how long it takes to find my favorite gene SERPINC1 and what kind of information is provided). I wonder what can be done about this ?

Usability is the last thing on any scientists mind, given that most projects are results based and not focused on the end user (other scientists using the resource).

the origin of sars

Anonymous — Fri, 13 Jun 2003 13:09:36 -0400

Despite a lot of hypothesis about the origin of sars indeed that their is a speculation that sars of the unimprtant coronavirus group in medicine could be originated in medical virology laboratories in countries which they have immense facility in creating gene maipulations or as a viral mutant or further more due to change in the ecology of viruses specially in heavily populated countries

Reference

chris — Tue, 27 May 2003 03:55:35 -0400

Sorry about that. Pubmed hadn't cited it yet when I posted. It's the Lancet, Volume 361, Number 9371 24 May 2003. Can't find in PubMed.And, fwiw, a pubmed search (via hubmed)on the man himself (bio note: he was a student and collaborator of Fred Hoyle's -- hence panspermia). Notice a theme to his papers?

In context...

Neil — Mon, 26 May 2003 23:28:58 -0400

Is there a link to the Lancet story? This has captured the imagination of the press of course; see Yahoo News for a brief story. A lot of media outlets are making the error of saying "Scientists say...", as if we speak with one voice. It should be pointed out that the main proponent is Chandra Wickramasinghe, who is a big fan of "life from space", panspermia etc. in general and a fairly controversial character.

recognition

chris — Mon, 14 Oct 2002 22:20:03 -0400

I think there's a very important distinction between awards such as the Oscars and the Nobel prizes. The former are in large part driven by corporate interests and fashions, whereas the latter are not. My impression of the Nobels is that awards are made after careful selection by a number of experts in the field. Given that the areas in which they are awarded are huge, and growing, the one problem is that many discoveries may be passed by or recognised much later (Barbara McClintock springs to mind - although politics was involved there).

All in all, I think they are a good institution. Recognition of merit, discovery, and/or services to humanity regardless of affiliations of any sort are a good thing, aren't they?

The citation for this year's Literature prize (Imre Kertesz, Hungary), reads: "for writing that upholds the fragile experience of the individual against the barbaric arbitrariness of history". More at the Nobel e-museum.

sharing and prizes

Neil — Mon, 14 Oct 2002 06:00:34 -0400

That would be an example of "new science versus old science" mentality.

What do people think of the Nobels? I'm generally not one for traditions or awards (think Oscars and Emmys - I mean, when does the stuff you like win?) But it seems to me that the Nobels generally "get it right", in terms of rewarding genuinely important research, albeit sometimes years after the fact. Is this related to the nomination process, which as I understand it involves a large community of prominent scientists?