Fiona Brinkman - Comments

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Tips for de novo bacterial genome assembly http://pathogenomics.bham.ac.uk/blog... Nice job on this Nick!

October 7, 2009 from Twitter - Comment - Like - Share

Been comparing notes with that blog post :) Also re-discovered the Velvet assembly reports at http://code.google.com/p... - Oliver Hofmann

Yes, those notes I'd sent you previously were heavily laden with tips from Nick! - Fiona Brinkman

ISMB/ECCB Stockholm 2009: Ruchira S. Datta

FFers open thread

June 26, 2009 - Comment - Like - Share

Surehy Breter, Pierre Lindenbaum, Cass Johnston and 7 other people liked this

I'm here and will be attending the BioPathways SIG. I figured there should be some place to say non-talk-specific things like "I've arrived!", so here it is. - Ruchira S. Datta

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Will be switching between DAM, BOSC and the BioPathways. Once I've figured out which talk is when ;) - Oliver Hofmann

Uhoh. I sense a lack of places to recharge notebooks. This is going to be fun during the session breaks.. - Oliver Hofmann

I forsee a problem with the SIG posts in FF - only one heading, and many, many speakers.... Hopefully will be OK for people following. - Allyson Lister

The projectionist kindly suggested I power up in the projection cubicle during the coffee break. - Ruchira S. Datta

Network is slowing down to a crawl for me. - Oliver Hofmann

Sitting at home, following the conference. Great job folks! My only wish is that there was some place where the speakers would upload their presentations. - Lars Juhl Jensen

Help! Anyone got a UK plug adaptor with them I could borrow for an hour or so? Will happily exchange laptop charge for beer/coffee. - Cass Johnston

Oliver, I've been having that problem too. There were some times when I had posted a comment and wanted to post another one, but the first hadn't finished posting, so I had to wait for the post to finish, hold my comment in my head, and also pay attention to what the speaker was currently saying... - Ruchira S. Datta

Talked to the organizers. They are aware of the problem, IT is looking into increasing bandwidth. Yay. - Oliver Hofmann

@Oliver well done! Perhaps we could ask someone to look into more power extension leads? :) - Allyson Lister

Anyone up for a FF lunch / dinner / drink at some point during ISMB? - Oliver Hofmann

Sounds good. I'm about to go orienteering, though, so will be out of reach this evening... - Ruchira S. Datta

Monday and Tuesday are the only "free" nights, with poster sessions going from 5:45 to 8:30 pm. Shall we just set Monday night for the FF meet-up? When would people want to leave the conference at the earliest? 8 pm? - Michael Kuhn

Monday's going to be busy meeting everyone; I'd probably try and stick around 'till 8pm. Meet at the registration booth close to the entrance at 8:15? Can decide on a venue depending on our numbers and whether people are willing to travel to the city center. - Oliver Hofmann

I think I would prefer 8:40. I have a poster. I haven't figured out yet whether it's Monday or Tuesday, but others might have posters too? Last year, at least, I was explaining my poster to people pretty much constantly until the poster session closed. - Ruchira S. Datta

Monday or Tuesday is good for me - either way, and any time is fine. It's a good idea! - Allyson Lister

8:45 on Monday then, same place (registration area)? Do we have any locals with suggestions? - Oliver Hofmann

ok - see you all in registration at 8:45 monday :) - Allyson Lister

If everyone has already seen Gamla Stan by that time, we could go to Södermalm--plenty of good restaurants. I'm staying there. - Ruchira S. Datta

@Ruchira: works for me as long as we have a guide to get us there :) - Oliver Hofmann

@Allyson There are lots of power extensions along the windows just inside the T hall. Let me know if those are still too full and I'll see what I can do about getting more. - Dave Messina

@Oliver The conference organizers have bought high-speed internet. Anyone can go to the registration desk for a free login. Spread the word! - Dave Messina

@Dave, yep, got mine this morning. World of a difference. - Oliver Hofmann

@Dave, any chance of getting extension cords to the other conference rooms? Starved for outlets at K21 :) - Oliver Hofmann

I'll be arriving today, would it be worth to pack a extension cords with multiple sockets? - Roland Krause

@Roland: This is always a good idea. Problem is that some rooms only have power on the stage and in the projection booth. - Michael Kuhn

Organizers also have extra extension cords for emergencies, but even the main conference room has no outlets. Best to recharge during the breaks, but that means leaving the notebook unattended... - Oliver Hofmann

photos from ISMB/ECCB, please put on flickr under tag "ismbeccb2009" - Burkhard Rost

The projectionist here just unplugged my power cord from their outlet and said none of us will be allowed to use their outlet; we'll need to use the outlets in Hall C. He said the organizers did not pay for extra outlets, so we will still have this power problem. - Ruchira S. Datta

Well, at least I'll be able to sit closer to the front where I can see better. - Ruchira S. Datta

Even the "free" network is considerably faster and more responsive today. Well… we'll see what happens when the first coffee break hits. - Johann Visagie

@Ruchira: Ouch. That's not going to help. We can get extension cords and use them in the smaller meeting rooms though. - Oliver Hofmann

@Johann agreed - I also think the network is faster today - Allyson Lister

I love the fierce, ofttimes violent competition for the limited resource that is power outlets during coffee break! - Johann Visagie

It seems a simple #ismb is the twitter hashtag of choice. Also note Burkhard's suggestion above to use "ismbeccb2009" as Flickr tag. (Hey! Flickr tags can has spaces! ;) - Johann Visagie

@Johann: Bring your own socket multiplier and you are loved by everyone ;-) - Oliver Hofmann

Any chance of leaving / recharging our desktops at the registration desk during the breaks? Would rather not leave mine in a conference room unattended. - Oliver Hofmann

Lonely FFer near the registration desk is looking for some chatting... anyone? - Egon Willighagen

Sure, I'll wander by momentarily. - Ruchira S. Datta

I'm sitting on the ground in front of the registration desk, waering a black t-shirt... - Egon Willighagen

Any poster presenters here on FriendFeed? Maybe you can start a new post in the ISMB/ECCB room and attach your poster PDF? - Egon Willighagen

Great idea, Egon! Not being at the conference, I would very much appreciate being able to see some of the posters on FF. - Lars Juhl Jensen

Lars, are you in Stockholm? - Egon Willighagen

What about special sessions, I do not see them here. - Diego M. Riaño-Pachón

I'm having a special FF sessions outside, but I am the only participant :) (after a nice meet up with Ruchira earlier) - Egon Willighagen

@Egon - shame - I was offline for lunch. At least I assume it was lunch you said that. FF doesn't put up the time each comment was made - so add times please if you're talking about meetups! Hopefully see most of you this evening after the poster session anyway :) - Allyson Lister

P.S. The network seems to have slowed down again. Anyone else notice, or is it just me? - Allyson Lister

@Dave thanks for the power extension cable - except for the main victoria hall (as we discussed) it's really helped a lot :) - Allyson Lister

@Allysin, I'm still around... in front of E.A.T. now.... - Egon Willighagen

@Egon - ah, but I'm in a talk! :) - Allyson Lister

@Egon, no I decided not to go this year - Lars Juhl Jensen

@Allyson: As half of the conference is probably sharing the username / password for the closed network I am not surprised it is slowing down :) - Oliver Hofmann

Maybe it is because I am happily uploading Jmol 11.7.45 to SourceForge ? :) - Egon Willighagen

@Allyson Glad to help! - Dave Messina

@Oliver Hopefully it's that rather than someone downloading Genbank. :) Still plenty of FREE logins for the closed wifi are available at the registration desk for anyone who wants one. - Dave Messina

Fun to see how quickly many of us have found a workaround for the 'Oops'... :) - Egon Willighagen

Is there a place for posting jobs/student positions available to ISMB attendees? (i.e. http://tinyurl.com/brinkma...) I'm not at the ISMB this year, so am definitely checking out FF and related resources and thank you all for your posts! - Fiona Brinkman

Does anyone know how to 'filter out' all group:ismbeccb2009 messages in my main feed? So that I can just open the ISMB/ECCB 2009 group in a separate window? - Egon Willighagen

Thanks to everyone - organizers, reviewers, presenters, friends, bloggers etc etc etc : I must away, but had loads of fun! :) - Allyson Lister

@Allyson, safe travels. @all, see you in Boston. Feel free to PM/mail me for tips where to stay, eat or party in the city. - Oliver Hofmann

nice meeting you, Allyson, and have a safe trip! - Ruchira S. Datta

I am leaving too, was nice meeting you all and have a good trip back. - Roland Krause

Conference finally closed. - Peter Menzel

i'm now at the Stockholm airport en route to Cambridge for another conference (!) http://www.functionalgenomics.org.uk/section... It was fun meeting some of you and microblogging together. Hope we'll see each other around at future conferences. Next year in Boston! - Ruchira S. Datta

@Egon: if you go to the ismbeccb09 room and click the "(edit)" link to the right of "Lists" then you can deselect it from your Home feed. - Lars Juhl Jensen

A top-ten of talks (well, not really - just the top ten of my ISMB posts based on number of hits). What was everyone interested in enough to click through to my blog? Find out: http://themindwobbles.wordpress.com/2009... - Allyson Lister

ISMB/ECCB Stockholm 2009: Roland Krause

Birds of a Feather session: Beyond microblogging, Wednesday, 1pm confirmed.

June 30, 2009 - Comment - Like - Share

Daniel Mietchen, Mickey Kosloff, James Taylor and 7 other people liked this

Thanks for setting this up, @Roland! - Allyson Lister

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Some thoughts I've had: Pre-annotation of papers and posters prior to the meeting, as is done by David Shotton in "Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article" at http://dx.doi.org/10... . Don't think it's automated, but you get the idea - and David Shotton gave a talk here this week (http://ff.im/4xwI9) ; and also Reflect (http://ff.im/4yVO1) - Allyson Lister

Also, how should scientists start with microblogging and social networking? http://themindwobbles.wordpress.com/2009... - Allyson Lister

Let's meet for the 4.15 coffee break at the coffee bar in front of K1, @Allyson and other interested people. If you have ideas, it would be good to prepare them. - Roland Krause

sounds good :) - Allyson Lister

http://ff.im/4BEXJ might also be of interest (Utopia ) - Allyson Lister

I COMPLETELY forgot about the meetup at coffee today! I'm sooo sorry! Was anything decided? Can you put up any summary points that might be of interest tomorrow? My apologies! - Allyson Lister

@Allyson: Wednesday. It's Tuesday :o) - Oliver Hofmann

@Oliver - I missed the pre-BOF meetup today at 4:15 at coffee - see above... :( - Allyson Lister

Oh. I did not even SEE that comment. Sigh. - Oliver Hofmann

No problem, we can meet over nibbles at the reception now. I can tell you what I have in mind. - Roland Krause

@Roland - I'm afraid I'm not available this evening. Morning? Or just write your ideas here? I'm a dork - sorry! :) - Allyson Lister

This should not take long at all, but please leave your ideas here. This is going to be an interactive session anyway, so we don't have to be all that prepared. My slides are more of a moderation prop than a standalone presentation. - Roland Krause

I would like to have some meta-discussion: why are we live blogging? How is this useful and how can we make it more useful? Does it mainly benefit those not attending the meeting or is it also useful as an archive of what has been said? - Michael Kuhn from iPod

Which room the BoF takes place? - Peter Menzel

In addition to what Michael Kuhn (@biocs) said, meeting microblogging can also benefit the presenter - giving them valuable feedback. Also links posted to papers, websites, etc. are great, to easily view more info about what someone is/was talking about. - Fiona Brinkman

I'll miss this, due to my time difference (Can. west coast) but I look forward to all your thoughts and thank you for setting this BoF up! - Fiona Brinkman

@Fiona - we'll make sure to post (maybe microblog!) the BoF :) Thanks for your input - benefits to the presenter is a really good point. - Allyson Lister

Last year at ISMB, even though I was already on FF I took notes as I habitually do, with calligraphic fountain pen. During the course of the intervening year I would find myself trying to refer back to those notes while in conversation with others, but had difficulty finding what I wanted in time. - Ruchira S. Datta

Paradoxically, I perceive myself as being slower when taking notes electronically than by hand (I think I tend to spend more time formulating them). But since we're doing this cooperatively, if one of us doesn't catch something another will. The notes will be searchable any time on the web; I won't have to dig up a particular file on a particular computer. The same effort provides the same resource for others. - Ruchira S. Datta

I did revert to the fountain pen at various points this year though! It's more reliable than depending on the availability of power, wireless, and FriendFeed. - Ruchira S. Datta

@Peter - the ISMB website tells me we will be in C8 for this session - Allyson Lister

The BioSysBio 2009 conference report (http://genomebiology.com/2009...) just came out (disclaimer, I'm an author). Simon Cockell had a wordle used (http://www.flickr.com/photos...), and FF and Twitter get a mention, if a short one: "A new feature for BioSysBio 2009 to extend participation in the conference was to a wider audience by communicating live... more... - Allyson Lister

Roland, where is the BoF going to be? - Michael Kuhn

The location is still given as C8. - Roland Krause

Set up an Etherpad for collaborative note taking: http://etherpad.com/EOOgB1Y27Z - Oliver Hofmann

I will be there from 12:40 onwards, if you have left suggestions here, please be there a little earlier for a quick roundup. - Roland Krause

Getting started. Mini-overview of past/current/future - Oliver Hofmann

Disclaimer for presentations -- what is allowed and what isn't (mail, blogging, film...) - Oliver Hofmann

Reference to Cameron Neylon's logos for presenters: http://blog.openwetware.org/science... - Allyson Lister

A need to make presenters aware of what might be distributed how - Oliver Hofmann

Reference to CSHL and recent "controversy": http://scienceblogs.com/genetic... - Allyson Lister

Conference blogging ideas from nature: http://www.nature.com/news... - Allyson Lister

Brief discussion of CSHL controversy - Oliver Hofmann

Journalists and bloggers should abide by the same rules at a conference - whatever those rules are - Allyson Lister

Classical blog posts, twitter and friendfeed: surprising how effective friendfeed is given it's basic nature - Oliver Hofmann

Find it quite difficult to make sense out of Twitter (best - wordle aka Simon Cockell?) - Allyson Lister

Oliver says FF isn't perfect, but it does have a very low barrier to access and start using - Allyson Lister

Where do personal opinions come into it? In general at ISMB we are all being polite. What level is acceptable? - Allyson Lister

Roland: the discussion culture in science has changed a litle. He read that 50 years ago they were having much more open discussions - Allyson Lister

Maybe people might be away from the conference and following remotely, or at the conference and shy - such people could pose questions on friendfeed, and then chair (who is monitoring FF) could ask them at the end of the talk - Allyson Lister

Differences to last year: increased depth of coverage (due to ISCB support, raised awareness?) - Oliver Hofmann

We all thanked the organisers from this year - Allyson Lister

ISMB people (Reinhard?) will do some basic stats of the coverage of this conference - Allyson Lister

Many of us bloggers feel that the first to benefit are ourselves - Allyson Lister

First person to benefit from blogging: the blogger - Oliver Hofmann

Live blogging especially useful for keynotes - for recording the presenter's thoughts.. and not always an accompanying paper available.. ? - Peter Menzel

Andrew: heavily blogged talks are more useful for external people than delegates - Allyson Lister

liveblogging is complementary to webcast etc as it takes less time - if you like the liveblogging and the blog posts after scanning, then you go and look at webcast - Allyson Lister

Also, people liveblogging tends to pick out the key points quickly - Allyson Lister

webcasting also has many time and technical issues - Allyson Lister

oliver: Perhaps much of the commenting is too sober. Not enough meta-information, e.g. "here is X's main competitor's paper..." - Allyson Lister

it would be nice to have more background - yes - Jim Procter

Roland: can you have two streams - one light, one serious. Allyson: but it would be difficult in practice, if you have to look at two different things - Allyson Lister

Three levels: factual information/transcript. notes to self, public commentary / context - Oliver Hofmann

Feeds are important feedback for the presenter ? - Peter Menzel

technical issues: there can be issues with internet / wireless - Allyson Lister

(Like right now?) - Oliver Hofmann

@Oliver - yep! Back now, though :) - Allyson Lister

Should we have TLAs or abbrevs to indicate personal comments or uncertainty? Maybe not TLAs (makes barrier for newbies) - how about single symbol at the beginning, e.g. '#' for personal comments - Allyson Lister

We should write up a boilerplate: what it means to liveblog; if you don't want it, then... (e.g. logo from Cameron) ;why scientists should liveblog; *suggest* that your FF account should link to something that identifies you; you might want to consider only posting things that you would be happy saying to people's face. - Allyson Lister

no legislation, though - don't want to force people to do anything - Allyson Lister

ISMB will certainly do it next year - Allyson Lister

imho: Official Facebook group etc. should be more advertised.. - Peter Menzel

@Peter - I agree - the embedded FF threads within the ISMB site were advertised, but more should have been made of them - it's quite cool to see! - Allyson Lister

Some great points made here - thank you! - Fiona Brinkman

see here for the Google Doc to make a write-up out of this discussion: http://docs.google.com/Doc... - Michael Kuhn

Fiona Brinkman › Comments