coComments related to mndoci

People are looking in the wron

2007-08-31T21:58:41.505+02:00

People are looking in the wrong place. The answer to people powered search is Lijit. You upload your trusted network into Lijit (del.icio.us network, blogroll, etc). Default search is across your network and their connections. That pretty much defines tacit trust in my eyes. It combines algorithms and people quite nicely.

Depends on the kind of granula

2007-08-23T07:11:13.303+02:00

Depends on the kind of granularity you want. At the level of "amidohydrolase" Pfam might do the trick, but at the level of identifying the unique combination of sequence, structure and lead family, this does have some unique information content.

YASARA looks good to. Never t

2007-08-19T19:40:07.845+02:00

YASARA looks good to. Never tried it but it was always intriguing as was VEGA which I last used about 7 years ago. Re DSViewer ... it got completely re-written a couple of years ago, so the performance should be better. It's essentially WLViewer resurrected. It does have more features than a lot of people need though, and is probably more useful if you are doing drug design. I have mixed feelings on PyMol. It's the best visualization software I've used, but I feel Warren has lost a lot of goodwill with the current approach, especially in the academic community.

Great post. Actually you'd be

2007-08-18T19:59:38.810+02:00

Great post. Actually you'd be amazed at home many spreadsheets still fly around and how much time is spent just re-formatting data. Perhaps, it's the cynical side in me, but I feel that bench scientists, while being more comfortable using computers than before are still not comfortable getting under the hood. I wonder if that will every change. I've actually seen it get worse over the years.

There was a similar paper by M

2007-08-16T05:52:28.810+02:00

There was a similar paper by Matt Jacobsen and co-workers (either in BMC or a PLoS journal) published a month or so ago. That said, this is quite impressive, especially the bit about transition states. Shoichet is quite a heavyweight in the molecular modeling world, which probably helped get this into Nature (plus the fact that they actually got a crystal structure as well). Even a couple of years ago, there was no way something like this would get published in nature.. The cool part ... this validates a lot of what we were doing at my first company over 5 years ago.

Whoops forgot to close the lin

2007-08-09T22:31:12.562+02:00

Whoops forgot to close the link. Could you please do that for me?

If I could pitch something tha

2007-08-09T22:30:45.964+02:00

If I could pitch something that was released just as I was leaving Accelrys. Discovery Studio Visualizer is the next generation of WebLab ViewerLight, and significantly more powerful. Best of all, it runs on Linux. IMO, PyMol is still the best, but unfortunately not as easily accessible as it used to be. Having used VMD through grad school (from version 1), I must admit to having a very soft spot for it. I think that it's selection syntax is what makes it as powerful as it is.

Welcome aboard. Great start!!

2007-08-09T22:26:18.671+02:00

Welcome aboard. Great start!!! and pretty pictures are always welcome :)

So far Scintilla is something

2007-07-04T06:58:42.441+02:00

So far Scintilla is something I am using primarily as a means of scientific discovery, via the "read" and "recommend" pages. I still think the "read" page, needs some design changes to make it more effective, but thumbs up to the effort. I actually use it every day.

Jeff Completely respect your

2007-06-24T21:33:03.495+02:00

Jeff Completely respect your consistency and opinion. I do still think that others are not quite the same. I don't think this is the last of the discussion on the boundaries between blogging, marketing and monetization.

I am somewhat on the fence on

2007-06-24T19:06:37.227+02:00

I am somewhat on the fence on this issue. On one side I understand why people are so pissed off. On the other hand, if the campaign had not been a Microsoft campaign, I am sure people would not have noticed (if it had been an Apple one, they might even have called it innovative). Are the bloggers endorsing microsoft's campaign? Yes Are they endorsing microsoft product products and services? Not really Can they carry that ad campaign on their sites? Why not? Perhaps the only mistake that was made was not disclosing the day the campaign started that they were participating in it, just to remove any confusion. Other than that, heck, it's an ad campaign, and not too bad a one at that.

In a lot of companies, ELN's a

2007-06-13T17:25:39.172+02:00

In a lot of companies, ELN's are becoming mandatory. What is missing is grassroots levels ELNs which can be used in academic research labs, etc. It's important for any number of reasons. Back in the day, I maintained a simple HTML notebook. If things like Rails existed, would probably have written something that could be more extensible. I know any number of wet lab scientists who would like ELN access and are sufficiently computer savvy to work with the coders to get something decent done. That would be a good place to start.

It's because they can't handle

2007-06-06T06:39:25.561+02:00

It's because they can't handle the new docx format. I think it is in an xml format that microsoft would like to see standardized, but it would be so much better if it was all in ODF.

From a third worlder with a fi

2007-05-21T22:35:43.038+02:00

From a third worlder with a first world blog, I can safely say that my blog does generate significant traffic from India, not in the least due to the fact that I am in the blog roll for nOnoscience, which to my knowledge gets a fair degree of traffic. In general though, you are right on the button. Outside of nOnoscience and BioHacking, pretty much every science blog I read is either based in North America or Europe, with one notable exception from Down Under. Topics of scientific blogging come up quite a bit in Indian blogs. The general feeling I get is that scientists, especially academics, do not think blogging is a worthwhile exercise, and is some form of narcissistic delusion. I might be jumping into hyperbole here, but its not that far from reality.

I am sticking with Twitter, es

2007-05-17T18:47:57.376+02:00

I am sticking with Twitter, esp since most of my connections are on it. As Michael said, not mission critical, and Jaiku does way more than I need.

This is good stuff. Can't wai

2007-05-14T00:07:40.678+02:00

This is good stuff. Can't wait to see more.

This is cool. Can't wait to se

2007-05-14T00:05:14.343+02:00

This is cool. Can't wait to see the rest

They need to move the main sit

2007-05-06T03:36:39.396+02:00

They need to move the main site over to that look n feel. It's much nicer

Yep ... iGoogle is the first t

2007-05-05T19:02:51.232+02:00

Yep ... iGoogle is the first thing I see every morning ... and often the last thing I look at every night ... that didn't sound too good did it :). I also track my Feedburner and Google analytics on iGoogle.

Hmmm I think this is one where

2007-05-05T18:39:16.215+02:00

Hmmm I think this is one where I will disagree. For my work and otherwise, del.icio.us has proven to be the most useful web service. I can't think of any other than I use (only Google). That said, I use it more like a bookmarking service (and the Direfox integration makes it very easy). In fact, other than the 20 websites or so I access daily, all my bookmarks are on del.icio.us (and many are private). I think the difference is, I rarely ever use the del.icio.us site itself. Everything is done in Firefox. Yahoo has done a terrible job with del.icio.us, IMO. The one thing that has improved .. the speed.

Can it be so hard for a panel

2007-04-29T19:05:26.088+02:00

Can it be so hard for a panel of experts to get together Getting the panel together is the easy part. Getting them to agree to a set of standards and have meaningful dialog on the other hand, that's another story. There have been some success stories, but for each success story, there are probably ten more failures. Scientists (I suppose all people) are good at talking about things, but not half as good as taking action.

I've been meaning to implement

2007-04-25T07:00:18.719+02:00

I've been meaning to implement OpenID on my own site and have been using it at a few others, notably Highrise. The usage seems to be increasing with the kind of support OpenID has in the tech industry. As far as social networks are concerned, I am with you. If all used OpenID, it would be soooo much easier.

Slideshare is quite cool. I u

2007-04-22T08:51:17.856+02:00

Slideshare is quite cool. I use it a bit when I want to get ideas on a subject or two (finding slides on marketing and investment is not too difficult). Finally put one of mine up there as well.

The Outlook thing was a showst

2007-04-19T08:27:13.948+02:00

The Outlook thing was a showstopper for me. Also, I agree with those who say that for someone like Mike, LinkedIn may not be useful, but for us lesser mortals, it's pretty darn useful. One has to be a little disciplined about it, but it's been quite useful for me and others I know, and not just for sales.

It's just a search history bas

2007-04-19T08:20:36.039+02:00

It's just a search history based recommendation engine. Probably something they cooked up pretty quickly, so while the timing is probably deliberate, they must have had it in the oven for a bit. A year ago this would have been seen as cute. I am a stumbler, although I never use the social features. I plan to use both, since the recommendation engine was pretty good. I wonder if Amazon would have been the ideal suitor for StumbleUpon? EBay just doesn't make sense

Back in the day when I used to

2007-04-18T19:08:40.057+02:00

Back in the day when I used to write a gazillion lines of Perl code daily, I still did it that way. Must have written a total of 5 packages. Most of the time, just re-use. Of course, Bio::Perl helped a lot :)

Been tumblelogging for a while after I heard about it on TWiT. It had a "I get it" feel to it, and given a choice between Tumblr and Twitter, I'd take the former any day.

That is why I like the concept

2007-04-02T16:11:07.366+02:00

That is why I like the concept of OpenID and some other related concepts. As Chris Pirillo put it once, are we really going to separate our friends by social networks (or IM clients).

David Belated thanks. The de

2007-03-29T04:39:20.611+02:00

David Belated thanks. The descriptions are working now.

exactly ... plus its fast with

2007-03-24T15:20:11.106+01:00

exactly ... plus its fast with those keyboard shortcuts

I did the same. Just didn't f

2007-03-24T15:18:42.380+01:00

I did the same. Just didn't fit the way I use things

Cool thread. My take Gmail -

2007-03-22T17:35:30.625+01:00

Cool thread. My take Gmail - I don't use any other email service anymore. Unfortunately I have to use Outlook at work. Docs/Spreadsheets. I use it for my Worldchanging blogging (to keep a record, since articles go through an editor). Otherwise mostly for jotting down stuff Notebook - I use it a lot to dump information, but find it a little limiting (no tags) Web Albums - Don't use, since I am married to Flickr Reader - The best thing since sliced bread Groups - Use it heavily in collaborative fun projects with friends, but we have switched to basecamp for the real serious stuff Calendar - Use it heavily (in fact all the time) Analytics - Use it a bit and like it. Does more than I need. Calendar integration into Groups and Gmail would complete things for me.

Way to go guys. Hopefully no

2007-03-22T03:41:56.772+01:00

Way to go guys. Hopefully no Digg effect :). Haven't seen anything. On the flip side, my descriptions are still not showing up :(

Yep, the Wordpress folk need s

2007-03-18T03:15:32.878+01:00

Yep, the Wordpress folk need some kind of super award for how good Akismet is. It's amazing how good it is. I've also noticed what kind of posts get spam. 90% of the spam is due to 10% of my posts.

The new theme rocks as does Ra

2007-03-14T21:06:26.126+01:00

The new theme rocks as does Radar. Just getting my feet wet. and that hack for Twitter quotes. Can't wait to try it out

I also found the historic part

2007-03-04T05:39:25.555+01:00

I also found the historic part funny, but since there is no such thing as "too much Fripp" who cares. For Service Pack 1 they should grab Trey Gunn and record him :)

I think most of us did and ove

2007-02-17T19:37:58.460+01:00

I think most of us did and overnight, Google Feedfetcher is the number 1 subscriber to my blog (34%).

But "disorder" doesn't sound t

2007-02-15T01:00:11.093+01:00

But "disorder" doesn't sound tough enough.

I promise I was not drunk when

2007-01-24T19:15:59.562+01:00

I promise I was not drunk when I wrote that comment (why can't upload include an automatic spellcheck)

I am with writhgt. I never li

2007-01-24T04:53:43.386+01:00

I am with writhgt. I never like the midichlorian concent either, but this is cool. May the Force be with you!!!

Wow .. that was very sudden an

2007-01-23T05:59:24.496+01:00

Wow .. that was very sudden and sad. I never tried the ad product, but their metrics product was very useful and I continue to use the blog editor. I wonder what happened cause all this unraveled very quickly.

Great question. I come from a

2007-01-17T08:28:54.178+01:00

Great question. I come from a generation where document management systems didn't exist. The biggest challenge will be bibliographies. I suppose you want a good check-in/check-out system. Unfortunately I have only used commercial or home-made DMS' You might want to take a look at this. At worst, there is a list of open source DMS options.

Sad all round actually. Poorl

2007-01-05T17:49:38.185+01:00

Sad all round actually. Poorly handled from the M&A perspective and the PR perspective. Not sure how this impacts PPP, but it hurts Performancing a lot and I liked their offerings.

Google calendar. First thing

2007-01-04T15:51:40.184+01:00

Google calendar. First thing I look at every morning. Multiple calendars, weather forecast, sharing, local events. Looks good and the integration with GMail helps. More than meets my needs. Someone asked earlier .. yes you can get reminders to your cell phone

I think comments greatly enhan

2007-01-01T04:45:49.442+01:00

I think comments greatly enhance what a blog really is, at least how I interpret it. That said, Seth Godin's blog is probably the one I know where I don't miss commenting. Perhaps cause I use it as a source of wisdom. Maybe the blog definition needs to be informally bifurcated into conversational blogs and informational blogs, the latter being comment free.

I couldn't care less for the r

2006-12-29T15:07:31.309+01:00

I couldn't care less for the real top 10. I do care for the list that was presented. It's much more indicative of how search trends were different this year than the last. We all know that the top 10 is likely to be the same mundane stuff year after year and mostly uninteresting. So while they could have been more clear, Google should probably stick to this zeitgeist format.