Bioinformatics stuff

terdon

13:00

@Faheem ?

OK

Faheem Mitha

hi

terdon

So, what do you mean about PlosOne? No proofs?

Faheem Mitha

@terdon yes, they don't give you proofs. they just publish the thing. nutty. and the editorial process is a mess. and they messed up my figures.

i think they would be kind of a last resort thing. though possibly better than a proprietary journal

terdon

@FaheemMitha proofs? They don't have a print version, why would they give you proofs? Strange about the image, I was fine when I published with them, LaTeX from start to finish

Faheem Mitha

@terdon oh, you've published with them?

terdon

13:02

Yeah, once

lol, this is a question you would not get in a biological journal:

Faheem Mitha

@terdon hmm, well, they don't want to change it afterwards, so it is basically publishing. they tell you to add a note or something if there is a mistake.

terdon

> p1, last line: did you define "V(D)J recombination"?

Faheem Mitha

@terdon a biological journal would not ask that?

terdon

@FaheemMitha ah, yeah, that's all the PLOS ones I think, they have some kind of stupid setup that won't let them change anything

Faheem Mitha

@terdon nutty. the one BMC journal I published in was more professional

terdon

13:04

@FaheemMitha no, since V(D)J recombination is a well known thing in immunology. You're talking about the recombination of the antibody genes right?

Faheem Mitha

i'll ask the annals editor if I should give Bayesian Analysis a shot.

terdon

I'm quite fond of PLosOne, I like their model

Faheem Mitha

@terdon right

@terdon the other issue is that i don't want to pay the pub fee. i don't have any financial support for this. i think some of these journals will waive the fee, maybe, but that could be a sticking point

terdon

In any case, if you want to publish in a bioinfo journal, I recommend you don't have any equations in the introduction, that should be in Methods or Results depending. Not in the intro though. Basically, as it stands, you paper has no intro, you dive straight into the juice of the matter

Faheem Mitha

Anyway, the idea is to publish in a goodish journal. not sure of PLOS one qualifies

@terdon good point. i'll bear that in mind.

terdon

13:06

@FaheemMitha ah, yes, can't help there, I've never published alone. All the open access journals need you to pay though cause they provide the paper for free

Faheem Mitha

@terdon right.

terdon

PLOS One had a pretty high impact factor, it's going down now but it's not as bad as all that, there have been some fine papers published in it

Faheem Mitha

Not the annals actually, so it is not 100%

@terdon ok

There are actually quite a few OA journals which don't make you pay

terdon

The basic advantage of PlosONe is that there's no scope so you won't be bugged by "not a good fit for our journal"

@FaheemMitha really? So who pays?

Faheem Mitha

@terdon exactly. that really is a pain

terdon

13:08

Where do they get the money?

Faheem Mitha

@terdon i think they are supported by universities. actually, running a journal is not that expensive if you don't want to make a profit

I'm not sure of the details.

if you think about it, all the work is volunteer, you just need someone to set up a web site. i think the annals does have a subscription option - you get more convenient access. their site is not directly open access, they dump stuff in arxiv. do you want a link with details?

terdon

@FaheemMitha nah, thanks, not my field. I think both the Oxford journals and the PLOS ones have special rules for helping authors with no financial backing

Faheem Mitha

@terdon yes, i'll throw myself on their mercy. :-)

@terdon ok, thanks fof the feedback

if you have further thoughts, i'm around. take a look at the reviews if you get the chance

terdon

> Bioinformatics authors have the option, at an additional charge, to make their paper freely available online immediately upon publication, under the
Oxford Open initiative. After your manuscript is accepted, as part of the mandatory licence form required of all corresponding authors, you will be asked to indicate whether or not you wish to pay to have your paper made freely available immediately. If you do not select the Open Access option, your paper will be published with standard subscription-based access and you will not be charged.

Faheem Mitha

@terdon right, with oxford bio, it would not be an issue in their default mode, which is proprietary

terdon

13:13

So it's a choice, either they charge you and give the paper for free, or they publish for free and sell access to the paper. Seems fair enough really.

Faheem Mitha

@terdon except, restricting access to the pape would hurt me.

the only one of my papers with no cites is the only one that is behind a paywall

terdon

@FaheemMitha yes. I also have moral issues with that. However bear in mind that the vast majority of your audience will have institutional subscriptions.

Faheem Mitha

@terdon that may be true, yes

is oxford bioinfo pretty mainstream?

terdon

It's the journal for Bioinformatics.

Faheem Mitha

@terdon ah, ok. i'll also bear that in mind. :-)

thanks.

terdon

13:16

PLOS Comp has a higher impact factor and molecular systems biology might do also, but the classic journal is bioinformatics

Faheem Mitha

so BMC bioinfo is a little lower level?

terdon

@FaheemMitha you're welcome. Good luck, I know how frustrating this shit is

@FaheemMitha Yeah, all the BMC ones are lower level

Faheem Mitha

@terdon appreciate the talk. again, if you have further thoughts, i'm around. you're right about the intro needing work

terdon

One tends to go there after being rejected by bioinformatics

Faheem Mitha

@terdon i see

@terdon so you think this paper could be a fit for oxford bioinfo, then?

terdon

13:17

Just remember that biologists like a good story, you should be able to explain the idea at least in English before you delve into details and give the math.

Faheem Mitha

@terdon i'll try to remember that. i assume the current version is too mathy from the get-go?

btw, how long will this room live for?

terdon

But they also don't get scared by math, for example, this is something I was a co author on:

Faheem Mitha

@terdon ok, clustering

terdon

Published in bioinformatics, it's a graph partitioning algorithm, but we also applied it to biological networks to predict multifunctional proteins ==> bioinformatics

Faheem Mitha

@terdon ok

terdon

13:20

And the room lives for a few days and will be automatically closed after X days of inactivity, don't remember the details

Faheem Mitha

@terdon ok.

well, thanks again. if you have further hints/suggestions about the paper, let me know

@terdon incidentally, you never did say why it is terdon.

just saw your email - is gmail or your address better for correspondence?

terdon

@FaheemMitha either, the institutional one is slower is all

Faheem Mitha

though i hate google, they harvest email content and then sell it to people i think

@terdon ok

terdon

and it's terdon cause that's just the username I typed out when installing one of my first Linux boxes back in university, just typed some random characters and have been stuck with it ever since :)

@FaheemMitha yeah, been trying to wean myself off of it...

Don't know of they do that (that sounds a bit extreme and too blatantly illegal) but yeah...

Faheem Mitha

@terdon well, i've got some content via facebook and linkedin which is difficult to explain any other way

@terdon ok. was hoping for a more interesting story :-)

terdon

13:26

@FaheemMitha are you kidding? You use facebook and you're worried about google? Come on!

facebook don't even try to hide that they use/sell/share your data

Faheem Mitha

@terdon i don't use facebook. but i have a page there. they spam me periodically

i created a page back when i was young and foolish. a few years ago

terdon

yeah me too, destroyed it later and now have a nameless one that lets me see my nephew's photographs and that's about it

Faheem Mitha

i haven't touched it in years, i haven't bothered to delete it because (a) facebook keeps all your data anyway and (b) lets people get in touch with me (in theory)

terdon

@FaheemMitha so, you're old and wise now :P

Faheem Mitha

though that has not happened yet

@terdon well, older and (more) jaded. :-)

terdon

13:28

:)

How old are you anyway? We're about the same age i think, I'm 33

Faheem Mitha

@terdon nope, unfortunately not. i'm 46

terdon

@FaheemMitha ah well, same generation :)

Faheem Mitha

@terdon :-)

terdon

(20 years to a generation)

Faheem Mitha

@terdon if you want to calculate it that way.

terdon

13:31

@FaheemMitha Hey, it's either that or I call you an old coot, which do you prefer? :P

Faheem Mitha

@terdon the former, please

terdon

thought so

Transcript for

Bioinformatics stuff