coComments related to pedrobeltrao

We might be too limited as ind

2008-05-23T20:38:42.384+02:00

We might be too limited as individuals to grasp any significant portion of what we already know. We have increased the pace of research by specialization and there is typically many more people working within a field than those serving as bridges. One thing that is improving tremendously is our capacity to find and dig into a part of knowledge that is new to us as individuals. This could in this context as problematic as knowing. If I am faced with a problem to solve I will typically search for the current solutions or best directions for solving this problem. If there is a better solution at the end of a totally different direction then I might not try it.I wonder if this could be tested by machine learning or some type of model (different agents, search accuracy ,etc).

This is very interesting. I'll

2008-05-22T22:24:13.100+02:00

This is very interesting. I'll put in another possible factor to take into account is the costs associated with communication. Another reason for the distraction in a fully connected network could be the attention spent on the communication itself. Still, we are very far away from the Borg hive mind :), there is no possible way for anyone to keep up with all that is being developed in any given field so there is still a lot of room for originality.

I am off to Europe on holidays

2008-04-25T00:10:52.933+02:00

I am off to Europe on holidays on the 5th :/ .. oh well, next year.

I am repeating a bit what I sa

2008-02-07T23:51:31.071+01:00

I am repeating a bit what I said in a comment to Deepak's post but what I think is the biggest limitation right now is awareness. How to get the right people to join an open project even for a short period of time. It could work for those problems where there is already a sufficient number of people with the right expertise tuned in to respond to a call.

As you mentioned we have discu

2008-02-07T17:46:21.741+01:00

As you mentioned we have discussed this many times before. It is one of those issues that I think everyone agrees on. It would be useful to have universal IDs for researchers but what is lacking is not the technology but the support of a lot of players on a standard (mostly publishers, databases and funding agencies). So in the case of OpenID for example how would it work ? The publishers would have to request to all authors of a paper to submit their OpenID and this information would be made available to the literature databases as metadata.

:) bad programmer here too. I

2007-12-21T21:05:11.898+01:00

:) bad programmer here too. I have an alias in the editor for that block that reads tab delimited files.

I wanted to leave a comment bu

2007-11-21T21:51:44.577+01:00

I wanted to leave a comment but I could not :), it is great to see more scientists blogging. It increases the chances that we might start getting more collaborations out of this.

That paper from David Baker's

2007-11-14T21:28:42.199+01:00

That paper from David Baker's group is really interesting. Unfortunately it was a bit of a scoop for something that has been under development in the lab where I did my PhD but it is an important advance. Regarding the criticisms on the computational methods I have heard something similar recently in regards to protein interaction prediction. The argument was if we can screen for the interactions why even try to predict it. How else will we ever learn the underlying mechanism if we are not trying to model them and predict them ?

I just got into the habit of s

2007-11-12T15:52:44.579+01:00

I just got into the habit of staring and sharing at the same time when I like something. I think it is just a matter of time before Google Reader implements something like this internally. It would also be nice to be able to send this information to Scintilla. I prefer to read in Google Reader but I would like to have a place where I would get some stats on what a group (lets say the bioinformatic crowd) liked or not.

It is also the highest traffic

2007-11-12T15:50:46.135+01:00

It is also the highest traffic spikes I get. Second highest must be Bora I think :).

@Katie: I work in Bioinformati

2007-11-10T17:07:56.630+01:00

@Katie: I work in Bioinformatics and as with most computer related work you can work from home although I don't think it is a good idea to do it too often, it disconnects you from the working environment. The repetition issue is also much less of a problem in bioinformatics. On the flip side I think it is much easier to scoop a bioinformatic project.

This is something that has bee

2007-11-07T17:37:15.312+01:00

This is something that has been on my mind a lot, mostly because of all the social network news and hype. Facebook is interesting but every time someone asks me about it I can't find a good example of how it can be useful (in a science/work related way). It does not help me to find interesting science news, papers, collaborators, manage projects, etc. Nature Network is slightly more useful in this respect but mostly because they are trying to make the forums more dynamic. In between Connotea, Nature Network and Scintilla it looks like they are going in the right direction but I have the impression that it is not there yet and I also don't have an idea on how they could make it more useful.

Thanks for the compilation. I

2007-11-07T17:22:40.370+01:00

Thanks for the compilation. I was thinking also of trying to do something like this but I have yet to stumble upon useful applications. One that I like is Feedheads . Anything I share on Google Reader is tracked by Feedheads in Facebook and if any of my contacts is also using these I can see what they share. If more people would use this it could serve also to rank top shared science related content (ex. papers).

Seaweed for crystallization ?!

2007-11-01T16:10:56.691+01:00

Seaweed for crystallization ?! wow :) congratulations.

Thanks for the effort it is a

2007-11-01T14:46:36.131+01:00

Thanks for the effort it is a really nice edition.

Lights,camera,action ! Once up

2007-10-18T17:45:46.464+02:00

Lights,camera,action ! Once upon a time there lived an hemoglobin in a land called far far way :).

That first thought is a huge d

2007-09-29T14:07:35.269+02:00

That first thought is a huge difference between bench work and bioinformatics. When we have some questions we can just search for the answers online. In bench work you can search for the protocols online too but the manual how-to and the little tricks that make it work with your working conditions are really crucial and are not easy to find. That is why JoVE (http://www.myjove.com/) or something similar can really make a difference.

Thanks for posting the slides.

2007-09-27T11:14:27.204+02:00

Thanks for posting the slides. It is interesting. This is still very much for very large data volume but maybe whatever they build around this (maybe a GBase segment for scientific data) could be use for lower data volume uploaded via net.

I usually say that parsing dat

2007-09-19T13:27:01.400+02:00

I usually say that parsing data is the bioinformatics equivalent to pipetting and preparing buffers. In our case it would much easier if databases and services were set up right. Can we play guess the method ? pSTY :)

Early days indeed. I was surpr

2007-09-18T11:44:36.169+02:00

Early days indeed. I was surprised that it started out with so little functionalities. Google page creator looks more like a presentation tool than this one. I would only create one directly there if I have no time to do in on a offline app. I think powerpoint is one of the few things I still like about Microsoft office :) I know this might sound bad ;), but the tools it has to make good looking slides are really ahead of open office.

That is a funny idea :). Natur

2007-08-20T14:02:45.239+02:00

That is a funny idea :). Nature Desktop Search (NSD), scraping your data from your pc and networked drives and making it available on Nature Network ;). "NDS has identified your SBML/MIAME/etc compliant files and they are available at the site for common use". The most immediate application of this could be papers. People who read/bookmarked/blogged about this paper were also interested in these others. Your contacts in the social network recently showed interest in these papers (options, show only if X people flag paper or in my listed topics of interest).

I'll put in another name, YASA

2007-08-19T18:25:17.693+02:00

I'll put in another name, YASARA (www.yasara.org).

I am really for this but witho

2007-08-13T18:04:50.606+02:00

I am really for this but without the support of the supervisors it is hard for young people. I will start my first posdoc next year and I will try to talk with my future boss about this to see how he feels about sharing ongoing results.

Perl does not really motivate

2007-08-10T23:20:49.374+02:00

Perl does not really motivate this. I worked with Java for a couple of months and I did it from the start. With Perl, it has been 4 years and I have almost to re-usable functions that I made myself.

Ricardo: If you have time you

2007-08-06T01:43:31.103+02:00

Ricardo: If you have time you can host the next month's edition. Anders: As Neil said, we don't have anything specific for Bio::Blogs but many of the blogs around these topics are listed in the Nodalpoint wiki (http://wiki.nodalpoint.org/). Nodalpoint is down right at this moment so I cannot link to the right page but you should be able to find it from there.

Another potential reason not t

2007-07-31T12:01:41.004+02:00

Another potential reason not to open source the code is simply competition in academia. A closed code or database can serve as a differentiation factor. It takes time to build some resources and this unfortunate credit system does not value how much a code or database is used but how many papers get produced in X impact journals. Even if people agree by principle that opening up research is morally correct the current reward system will tend to push people to secrecy.