nodalpoint.org - Story - Comments

the context is larger than the post

seidel — Mon, 26 Nov 2007 15:45:46 -0500

I think it's totally kosher. The person was juxtaposing similar pieces of information. It's something we all depend on to be informed, and a reason for allowing comments. He may be taking some of the attention off your specific work, but he appears to be informing you of an alternative tool set you may not have known about. If he was pointing to a commercial alternative, that presumably has marketing resources behind it and therefore doesn't depend on mention in a weblog, I would find the comment annoying. Alternatively, if you were talking about a pretty new wedding dress design, and someone piped up about their own lovely new design, I might see some ruffled feathers. But just as comments are "weak connections" between pieces of information that can be positive or negative, it doesn't take a very thick skin to put up with comments that direct attention elsewhere.

Easy tiger

chris — Wed, 21 Nov 2007 10:52:58 -0500

I didn't think Bosco's reaction was unreasonable given the comment (YMMV, natch). The comment is rather poorly written, but I agree with Neil's assessment that it's harmless and probably just trying to be informative.

No

tiagoantao — Wed, 21 Nov 2007 09:52:03 -0500

I do think that the comment is fairly reasonable, and helpful to anyone that is looking for a Java solution to the same problem.

On the other hand, and in full honesty, your reaction seems borderline unreasonable and really inviting people not to comment on your entries.

kosher

dalloliogm — Wed, 21 Nov 2007 05:12:53 -0500

What does it means kosher? :)

I also think that comment is fine: I couldn't understand with which license that software is released, but it seems that it's a freely downloadable library.

Let's say you are a java programmer looking for a program that does the same things as yours: you will find that comment very useful; and your blog has twice the probability to be found by someone using google, because it's useful both for python and java programmers.

Moreover, think that if that software is really downloadable for free, the author of the comment doesn't gain any money if it's downloaded: you hardly know his name. Instead, you could ask him how they have implemented the algoritm, and exchange feedback, maybe on your blog.

Comment etiquette

Neil — Tue, 20 Nov 2007 21:39:43 -0500

Leaving aside that your solution is clearly superior, since Python is the language for structural bioinformatics, whereas Java is good for nothing :)

I think the commenter just needs a lesson in how to write comments. Something along the lines of: "Hi, for those who prefer to program in Java, I've written a set of classes called bioshell to perform many tasks, including RMSD calculations. Check it out if you're interested."

There will always be "me too in my language of choice" comments. They're best ignored, since they don't contribute to discussion of your original post.

I think it's fine. All of

eweaver — Tue, 20 Nov 2007 21:17:50 -0500

I think it's fine. All of opensource is working on the same problem in the end; it's a backhanded sort of collaboration, really. I usually just ask them why they think their solution is better.

The Broken Double Helix

Duncan — Mon, 29 Oct 2007 14:02:32 -0400

There is a good overview of the media-furore surrounding Jim's recent trip to the UK over at the molecular systems biology blog...

partial trageted assembly from trace archive

Hardip — Thu, 25 Oct 2007 03:28:05 -0400

Hi there,

have u tried using tracembler available at . i am also trying to achieve the same goal as you and currently designed a very crude perl program which can do the job but takes lot of time. And mainly the time is taken for reading database file for extracting the sequences for which i m planning to use fastacmd. let me know if u need to use the copy of the script that i have right now. it will require few modifications but i can help u with that.

Another boo-boo

chris — Tue, 23 Oct 2007 11:09:35 -0400

Yes - he's rather famous for these. When the Jimome was announced at the Biology of Genomes at CSHL in May, he gave an impromptu little homily before the keynote speeches. In his usual rambling style, he trotted out a number of comments which made his audience (or at least me) very uncomfortable - not least in reference to his son Rufus, who has a rather rare form of depressive (?) schizophrenia.
I wonder if his suspension by the CSHL Board is a prelude to his stepping down, or a slap on the wrist?
I will point out though that CSHL was a backwater when Watson took over; he attracted funding and donations and turned the place around. He still has enormous pull with private donors (eg the construction currently under way at a cost of ~$100 million).

out of his depth

seidel — Mon, 22 Oct 2007 12:45:56 -0400

I saw him speak in Berkeley where he made some of the remarks listed above, including an admonition not to hire fat people or accept them as graduate students because "...they are lazy, and too happy to work hard." The article in the independent gets it right when it describes him as out of his depth on the issue. Scientists can point to data that might be socially uncomfortable or non-PC and that's one thing, but he gets it wrong and throws in personal anecdotes as evidence - which throws all objectivity out the window, and simply paints him as a bigot. Aside from the content, the fact that he can't tell the trajectory of his own remarks disturbs me. I feel bad for Cold Spring Harbor. I hope they don't suffer any fallout (i.e. funding backlash).

simulaid

bosco — Thu, 16 Aug 2007 13:23:16 -0400

I downloaded it but couldn't get it to work properly for NAMD to AMBER.

Simulaid

Animesh — Thu, 16 Aug 2007 10:46:02 -0400

I have no idea about converting trajectories, but people talk about using Simulaid [ http://inka.mssm.edu/~mezei/simulaid/ ] for similar stuff, did you check it?

Looks familiar

Neil — Wed, 15 Aug 2007 09:52:19 -0400

Good to see that file format conversion is a full-time preoccupation in structural biology as well as for people working with sequences. Nice how-to.

Just a wild guess, but I'm

Greg — Tue, 14 Aug 2007 14:11:00 -0400

Just a wild guess, but I'm thinking this particular piece will not have the same broad impact of "Notes to a young computational biologist". Nonetheless, I am thinking that maybe your posts on these topics have brought a few more structural biologists into the world of blogging :)

Nightmares

mndoci — Tue, 14 Aug 2007 14:09:44 -0400

And I shudder at the memories of trajectory formats.

We should start a movement for MD standards, as in Force Field standards, trajectories, etc etc.