coComments related to What You’re Doing Is Rather Desperate

This is my first time reading,

2007-08-06T01:42:26.103+02:00

This is my first time reading, and …wow! Bio::Blogs really rocks.Is there any easy way to get a nice list of the cool bio-blogs that people submit stories from? Maybe even as OPML files?Thanks AndersAnders

Coooooool, BB RoCkS :) Thanks

2007-08-06T01:42:18.603+02:00

Coooooool, BB RoCkS :) Thanks guys!Animesh Sharma

I’d suspect that only bioinfor

2007-08-06T01:41:57.769+02:00

I’d suspect that only bioinformatics pros are eligible to host, right? I’m still very very new to this but am interested in hosting… on day :)If there is no volunteers, I can give it a go…Ricardo

I think the environment is les

2009-03-24T03:56:31.510+01:00

I think the environment is less reliable in biology than in computer science. If you re-run a compile you will (usually) get the same thing – more to the point you’d be annoyed if you didn’t because ’something is wrong’. Something not working is a pretty common occurance in your average wet lab so all procedures are a bit more contingent and a bit more local. But you’re point about culture is dead on. These things create a reinforcement loop where the end result is ‘Why bother putting up protocols seeing as they probably won’t work for other people’ or, worse ‘After all that work why should I give it away’. I would say working with computer scientists has its own challenges. People do look at me strangely when I try to use the terminology. To be fair this is more what happens in person than on the web which is much more friendly and open. Or is that just because I can’t see your expression? :)Cameron Neylon

A very good post, thanks. This

2008-09-24T16:00:12.763+02:00

A very good post, thanks. This is exactly what I’m experiencing. Whatever the reason for the 100%-attitude and ingroup vs outgroup behaviour it makes working for biologists difficult as a computer scientist. They, in turn, don’t know the “working” culture in computer science and think we aren’t really working but rather playing. Which might contain quite a bit of truth.Cameron is right but if biologists were like computer scientists then you would find tons of very detailed descriptions on the web and a newgroups for every strange technique with a core group of 5-10 experts that are happy to answer questions. Even the water at Bath can be analysed and once it’s part of an FAQ it’s not a mystery anymore. But this kind of reasoning seems to be difficult in biology or maybe there are simply more possible conditions to try than in computer science? No clue.max

I think part of it is that it

2008-03-28T02:03:54.016+01:00

I think part of it is that it is really hard to replicate and transfer difficult techniques. So while it is (relatively) easy to pass around, or replicate, say a perl script, a wet lab bench protocol, no matter how careful the person who wrote it down, could still be missing crucial details (this experiment doesn’t work in Bath because the water is too hard – and no I’m not kidding, this happens). So ’so-and-so is the world expert in system X’ really translates to ‘if you want to do this, go and learn in their lab’ then take it home and iron out all the extra issues that appear. The question of openness revolves around how willing they are to let you do this. Which is not to say that the availability and usefulness of good protocols couldn’t do with a lot of improvement.Cameron Neylon

I have to confess that the ter

2009-09-20T01:06:36.107+02:00

I have to confess that the term has grown on me since I first posted. It sounds like a line from : “I have a tremendous sense of unfoldedness”.nsaunders

It seems perfectly cromulent t

2009-09-20T01:06:27.774+02:00

It seems perfectly cromulent to me. In fact, I’d say that the study of unfoldedness embiggens structural biology.Jonathan Badger

But “disorder” doesn’t sound t

2009-09-20T01:06:19.441+02:00

But “disorder” doesn’t sound tough enough.Deepak

But is it a neologism?
2009-09-20T01:06:11.108+02:00
But is it a neologism?chris

The only noteworthy post conta

2009-09-20T01:06:02.775+02:00

The only noteworthy post containing ‘have not read the paper’ in 2007. Hopefully.Roland Krause

Hi Neil – although its not ope

2009-06-30T08:17:32.309+02:00

Hi Neil – although its not open source, we’ve just started using “Basecamp” (http://www.basecamphq.com/?ref=free) for a project on surfactin. Unsurprisingly the idea for using this came from the physical scientists and not from me! The free version provides a web-based platform for what is essentially a closed chat room. I’m still getting used to it, but the functionality is quite good. I’ve yet to use its document system in anger, but I’ll let you know how things progress. However, there is still the problem of trying to get people to actually work on the document (perhaps there should be a web-button that allows connection of their desk chair to the nearest mains supply?) or a system for dealing with the deliberately obtuse…Simon Baker

Matthias: that all sound excel

2009-04-09T23:40:23.388+02:00

Matthias: that all sound excellent. You have a project there that just keeps growing and developing. I’ll keep an eye on the latest features.nsaunders

Neil, thanks for this post, it

2009-01-18T14:03:14.467+01:00

Neil, thanks for this post, it hits a critical nerve. I agree that a plain text markup language such as LaTeX combined with a server-based versioning system and good doc comparison would be ideal for collaborative writing of scientific documents. Unfortunately, this isn’t an option for many people since, as noted in a previous post, the whole process “feels” to techy and is daunting and too complex for many scientists. However, I think that a wiki-like web-based software (that uses a simple markup language) could lower this barrier substantially.With regard to refbase, we have plans to better support the process of collaborative manuscript creation (which is a frequently requested feature). People could attach new manuscript versions to a database entry (which would be invisible to the public until its final) and include their comments. This would be more of a shared & commented manuscript repository that would be always accessible by all group members, but keeping it simple will help to get everyone actually using it. So manuscript editing would still be done offline (using your favourite tools) and the type of documents (.tex, .rtf, .doc, etc) could be freely chosen. Ideally, I’d like to integrate something like this with a versioning & document comparison system.Matthias Steffens

Probably overkill, but I’ve be

2008-10-29T05:26:05.546+01:00

Probably overkill, but I’ve been considering using an internal manuscript tracking system – like journals do. They track versions, support up/down load of files, etc.Ultimately, the main question you have to ask is whether you want to support parallel editing. If so, you need a text-based versioner of some sort. Tex format can be mostly converted into rtf, so perhaps the best solution is to use that? I’m assuming that trickier aspects of the document, such as display items, will be collated by the lead author. Even if they are not tex-savvy, there may be higher-level tex editors which will help them put these things together.chris

I’ve looked into this from tim

2008-08-08T21:48:56.625+02:00

I’ve looked into this from time to time also, since I hate messing about involved in the email-edit-email cycle that goes on when collaboratively writing a paper. Rather than just having another way of passing back and forth documents (ie shared storage), I’d really like proper collaborative editing.I think a wiki is ‘theoretically’ a good solution which could be very powerful for collaborative writing of scientific papers, but typically wikis don’t integrate cleanly with Word/Endnote etc. Older academics are unlikely to change their ways, and even if they did they would certainly want decent offline editing. One project that is at least attempting to solve this problem is the UniWakka wiki (http://uniwakka.sourceforge.net/HomePage), which has OpenOffice import and export, and the ability to import a BibTex database of references and cite them. I think in reality, users would have to be very disciplined with their use of OpenOffice so as to avoid creating documents that don’t import to UniWakka correctly. I’ll be watching closely to see what you find .. :)Andrew Perry

I’ve actually used Google docs

2008-05-19T13:11:47.704+02:00

I’ve actually used Google docs quite a bit for document collaboration, but how do you handle citations and other material? If one could do what alf suggests then you’d be in good shape.Neil, my life is already my google personalized homepage (with multiple search engines :) ). Welcome to the club!!!Deepak

AbiWord also has a collaborati

2008-02-28T03:34:38.783+01:00

AbiWord also has a collaboration server, where you edit the documents within AbiWord. There’s a bit more information here: http://uwog.net/news/?p=47 alf

Yes, Google Docs is pretty goo

2007-12-08T18:57:29.862+01:00

Yes, Google Docs is pretty good for collaborative editing. For citations/references, I’d like to be able to invite a bot – connected to an online bibliography database/manager – to collaborate on a document, and have it automatically format the references.alf

That’s a pretty good idea. Yo

2007-09-18T11:20:20.941+02:00

That’s a pretty good idea. You know, I’ve only just signed up for a Google account. When I last checked (a long time ago), their accounts were much more limited. Now it looks like you can do “Google everything”.Now I’ll probably spend several hours importing my life into my Google homepage. Thanks Pedro ;)nsaunders

I have been using Google Docs in my current collaboration work. For me it has almost everything required. The only thing that I am missing is a chat box (like the have in google spreadsheets) and a way to deal with references. Zoho also has a online document management tool.Pedro Beltrao

Thanks for that. Spent the af

2007-04-08T18:06:03.099+02:00

Thanks for that. Spent the afternoon playing with MyDMS, which I quite like so far.nsaunders

Good to meet you Neil, give us

2008-07-26T14:54:10.738+02:00

Good to meet you Neil, give us a shout if you’re in the Bay Area. IanIan Holmes

It was great meeting you as we

2008-07-26T14:54:00.738+02:00

It was great meeting you as well, Neil. Have a safe flight back home! :)Mauricio

I’ll be at Manchester airport

2008-07-26T14:53:50.738+02:00

I’ll be at Manchester airport for about an hour at 7:30 “this morning” :) Not sure about the way back down yet, will let you know.nsaunders

Ditto, when and how long are y

2008-07-26T14:53:40.738+02:00

Ditto, when and how long are you in Manchester for>Duncan

If you’re got some spare time

2008-07-26T14:53:30.738+02:00

If you’re got some spare time in Manchester, would be great to meet up.Mike

Nice having you here in TO and

2008-07-26T14:53:20.738+02:00

Nice having you here in TO and finally meeting you. Hope to see you soon. Mrs Nuin said “Hi”.CheersPaulo

> how long before paper cop

2009-02-15T02:05:06.465+01:00

> how long before paper copies of all journals are considered quaint and obsoletewhen major journals move to Open Access model. there are still some journals my library subscribes in print form only. sigh.Kevin

With screens the problem is fo

2008-07-15T09:32:29.368+02:00

With screens the problem is form factor. I admit that I read all technical material on my screen, but I’d rather use my laptop with the laptop on my lap :). Maybe they will design a reader that is (a) < $200, (b) looks good and (c) uses multitouch :)Deepak

You can add these type of link

2007-12-13T14:59:32.271+01:00

You can add these type of links yourself to any paper with this greasemonkey script: http://baoilleach.blogspot.com/2007/10/bring-pdb-codes-to-life-on-web-pa baoilleach

> how long before paper cop

2007-12-13T14:59:22.271+01:00

> how long before paper copies of all journals are considered > quaint and obsoleteThe moment people stop printing out PDFs to read later. ;)Euan

That’s wonderful actually. Ju

2007-12-13T14:59:12.271+01:00

That’s wonderful actually. Just the kind of thing that makes so much sense that no one does it, but Nature does grok the web these days.Deepak

Brian makes some good points –

2009-04-05T08:28:33.556+02:00

Brian makes some good points – follow the link in the comment above this one. Question: is “freeform” good, or should biologists strive to bring structure to their wetlab data, even before doing the experiment?nsaunders

a comment, Curtis ConnectedBases :: Electronic Laboratory Notebooks don’t work in the Wet-lab

No :) It would be nice to have

2008-05-09T12:57:06.364+02:00

No :) It would be nice to have some data though, rather than just me saying “they’re all rubbish”. Good project for wiki collaboration.nsaunders

Do you have the time for creat

2007-11-26T02:11:22.768+01:00

Do you have the time for creating an overview of the ELN tools you compared? This would be very useful for being able understanding the detailed arguments.Cheers, JoergJoerg Kurt Wegner

Very nice post. I agree that p

2007-06-13T17:25:19.172+02:00

Very nice post. I agree that paper notebooks are ridiculous in the computer age. While nearly every aspect of the modern research enterprise changes quickly, the lab notebook hasn’t changed in over 100 years. A labmate and I have also been spending a fair bit of time trying to come up with a good ELN solution. Your points are exactly what we have been thinking about, how would we design one from scratch? A key aspect of the modern electronic notebook should be data sharing and communication. Everyone involved in a project should be able to view and comment on recent results. One of the first steps we have taken is to get into the Web 2.0 arena by starting a social networking and social bookmarking website for scientists. We are hoping this site will start to improve communication among researchers. It’s at JeffsBench.com, please check it out. Maybe we will try to do an ELN next.Curtis

I wonder too. The closest tha

2007-06-13T17:25:09.172+02:00

I wonder too. The closest that I’ve found is the EMSL Collaboratory, which is DOE-funded. Unfortunately their efforts at an ELN require an advanced degree in Apache Tomcat administration before use.Similar problem with structural genomics – lots of people with the same requirements (target selection, workflows, data storage) – yet no one standard software solution.nsaunders

Absolutely. What’s missing mo

2007-06-13T17:24:59.172+02:00

Absolutely. What’s missing most at the moment in computational biology/bioinformatics is dialogue between the “computer people” and the “wet lab people”. We need more people who can speak both languages and who have the enthusiasm to keep prompting the biologists to participate; they are notoriously reticent ;)nsaunders

I agree that there needs to be

2007-06-13T17:24:49.172+02:00

I agree that there needs to be some kind of new system for lab journals, but how many of your colleagues feel comfortable with using such a tool or more specifically computers in general? Its like you said, “they don’t think about the software”. Every biologists who is in Bioinformatics starts to envision these beautiful tools that can be built for them but do not realize the time and work necessary for their development. Plus they do not realize commitment on their part to learn and faithfully use such a tool to further progress its development and functionality. I agree that we should be looking into such tools for the further progression of our respectable fields I just want to emphasize that when these tools are built Biologists who desire the tool should be included in every step of the development process.Ryan Castillo

I wonder why no major focus gr

2007-06-13T17:24:39.172+02:00

I wonder why no major focus group (NCBI, EBI, MPG, EU) has ever started a serious project on ELNs. It would bring so much to help scientists organizing data in the days of genomics, to secure reproducibility, etc. However, you probably need a strong group to get the project to some serious stage.Roland Krause

Cool I be waiting for that ELN

2007-06-13T17:24:29.172+02:00

Cool I be waiting for that ELN to dl and use! am also looking for a good system to intro to my colleagues who might be averse to steep learning curves…kevin

Neil hates social bookmarking

2009-06-23T03:19:36.630+02:00

Neil hates social bookmarking and then likes it (more) bbgm podcast #4 is available

Neil hates social bookmarking

2009-03-28T12:01:47.695+01:00

Neil hates social bookmarking and then likes it (more) bbgm podcast #4

Bill, I agree that the unalog

2008-12-31T21:43:58.760+01:00

Bill, I agree that the unalog beta disclaimer is a bit worrying, however, it may be just their standard disclaimer (I mean isn’t this true for any online service?) or a left-over from the early days. In any case, I’m sure Dan Chudnov would be happy to clarify the status and future plans for unalog.com. -mMatthias

Unalog looks great, but the no

2008-10-06T08:26:09.825+02:00

Unalog looks great, but the notice on the bottom of each page worries me a little: “this beta service might go down, go away, or lose data at any time – be warned”.Bill

I just checked and I have 3,60

2008-07-11T18:08:20.890+02:00

I just checked and I have 3,602 sites bookmarked at delicious. I’ve probably checked other people’s bookmarks five or six times during the months I’ve used it. I teach in a different town, I work as an online reference librarian, and I find it indispensable. For example, I was subbing one day when a student said, “I need an online resume site.” I went to my delicious page and pulled up the 7 sites I had under “resume.” We chose one, she created her resume, and I later copied the links and emailed them to her teacher. When I run across something one of my kids might like, I tag it “show[name]” and when they’ve all seen it, I delete the tags. I had no interest in uploading all my bookmarks at once. I *wanted* to check them one by one to make sure they were valid and to add annotations, so that aspect of delicious didn’t bother me. Delicious makes me happy.onlycrook

I’m not using any social bookm

2008-04-16T03:50:31.955+02:00

I’m not using any social bookmarking site, pretty much for the reasons you’ve mentioned above (though the previous commenters have made some valid points). *If* I’d use social bookmarking, I’d go with unalog made by Dan Chudnov. It’s wonderfully clean and simple, and it’s backed by very smart guys from the library community. –mMatthias

My main social bookmarking sit

2008-01-20T12:32:43.020+01:00

My main social bookmarking site is connotea because it has the ability to recognize web pages with scientific papers (using doi or pmid…). You can upload a batch of bookmarks once logged using this page : http://www.connotea.org/upload , see http://www.connotea.org/guide#importris : it can take as input firefox bookmarks. Time to time, I also synchronize my connotea bookmarls with del.icio.us . As said Stew, their ‘network’ option is really powerful for knowledge discovery (e.g. http://del.icio.us/network/lindenb?setcount=100). It also gives an API to upload many bookmarks.PierrePierre

coComments related to What You’re Doing Is Rather Desperate

This is my first time reading,

Coooooool, BB RoCkS :) Thanks

I’d suspect that only bioinfor

I think the environment is les

A very good post, thanks. This

I think part of it is that it

I have to confess that the ter

It seems perfectly cromulent t

But “disorder” doesn’t sound t

But is it a neologism? 2009-09-20T01:06:11.108+02:00 But is it a neologism?chris

The only noteworthy post conta

Hi Neil – although its not ope

Matthias: that all sound excel

Neil, thanks for this post, it

Probably overkill, but I’ve be

I’ve looked into this from tim

I’ve actually used Google docs

AbiWord also has a collaborati

Yes, Google Docs is pretty goo

That’s a pretty good idea. Yo

I have been using Google Docs in my current collaboration work. For me it has almost everything required. The only thing that I am missing is a chat box (like the have in google spreadsheets) and a way to deal with references. Zoho also has a online document management tool.Pedro Beltrao

Thanks for that. Spent the af

Good to meet you Neil, give us

It was great meeting you as we

I’ll be at Manchester airport

Ditto, when and how long are y

If you’re got some spare time

Nice having you here in TO and

> how long before paper cop

With screens the problem is fo

You can add these type of link

> how long before paper cop

That’s wonderful actually. Ju

Brian makes some good points –

a comment, Curtis ConnectedBases :: Electronic Laboratory Notebooks don’t work in the Wet-lab

No :) It would be nice to have

Do you have the time for creat

Very nice post. I agree that p

I wonder too. The closest tha

Absolutely. What’s missing mo

I agree that there needs to be

I wonder why no major focus gr

Cool I be waiting for that ELN

Neil hates social bookmarking

Neil hates social bookmarking

Bill, I agree that the unalog

Unalog looks great, but the no

I just checked and I have 3,60

I’m not using any social bookm

My main social bookmarking sit

But is it a neologism?
2009-09-20T01:06:11.108+02:00
But is it a neologism?chris