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Tony Haines |
Message #99680, posted by Loris at 16:17, 9/3/2007 |
 Ha ha, me mine, mwahahahaha
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OK, so you guys probably don't know, but one of the things I've been doing over the last year or so is writing a program to draw nice maps of annotated DNA sequence. That is, it draws a diagramatic representation of the features present in a DNA sequence, it doesn't render DNA molecules.
Its unlikely to be useful to your good selves; the intended users are predominantly molecular biologists, geneticists and the like. It is written in Perl under Linux, uses ImageMagick, and will be web-accessible.
So my end is mostly done - I've written the program, apart from the odd bug-fix, and am working on the docs. My cousin is doing the web interface.
So what is the problem? Well, I need:
1) A name,
2) A logo.
Regarding the name, the current forerunner is AnnoDraw (~annotation draw), followed by Genodraw (~genome draw), and the current place-holder EMBL2image (The annotated sequence files are in 'EMBL format').
Does anyone have any better ideas?
It also seems that in order to be successful that nowadays a project needs a good logo, ideally of a cute furry mascot. I'd quite like some sort of british-native animal, but I'm willing to be swayed from that. Any suggestions about this, or how to go about it?
(I don't have even 200 pounds to get these designed, the money I got for doing this was used up ages ago.) |
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Phil Mellor |
Message #99681, posted by monkeyson2 at 16:23, 9/3/2007, in reply to message #99680 |
 Please don't let them make me be a monkey butler
Posts: 12380
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WEMBL (The W standing for Web).
You could use a picture of a Womble. |
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Richard Goodwin |
Message #99682, posted by rich at 16:30, 9/3/2007, in reply to message #99681 |
 Dictator for life
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Wombles look a bit like badgers, which is a non-fictional native animal?
________
 Cheers,
Rich.
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Phil Mellor |
Message #99684, posted by monkeyson2 at 16:54, 9/3/2007, in reply to message #99682 |
Please don't let them make me be a monkey butler
Posts: 12380
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What about an extinct one?
http://en.wikipedia.org/wiki/List_of_extinct_animals_of_the_British_Isles#Mammals
Edit: an unfortunate URL, there: http://www.archive.org/details/britishanimalsex00hartiala
[Edited by monkeyson2 at 16:57, 9/3/2007] |
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Tony Haines |
Message #99697, posted by Loris at 19:04, 9/3/2007, in reply to message #99682 |
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Posts: 1025
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I have been considering the badger for it. (-) TB connotations. (+) Harry Hill connotations. (+) stripey (-) monochrome.
I don't want to use an extinct or endangered animal.
Maybe an invertebrate? I'm fond of snails, spiders, woodlice, harvestmen, millipedes...
Here is a fantastic tool, but that logo is rather ... functional.
Maybe I'm being swayed too much by firefox and linux. The one thegman pointed to for Haiku os, on Drobe, seems rather elegant. Something in the same vein would be fine, I guess. I did once make a nice (IISSM) image for my wife's ebay selling, which had butterflies on it.
Hmm. I'm almost tempted to use Hotei/Budai (the 'laughing buddha'; a god of god of abundance and good health), although Benzaiten (Chinese god of goddess of knowledge, art and beauty) might be more appropriate. Maybe a two god set...
If there was an acronym for the name that would help, provided it wasn't one of those tortured ones. I wouldn't put too much emphasis on the EMBL part of it; the program will only ever be a tiny tool compared to the might of the EBI databases. |
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VinceH |
Message #99702, posted by VincceH at 22:49, 9/3/2007, in reply to message #99680 |
 Lowering the tone since the dawn of time
Posts: 1600
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Regarding the name, the current forerunner is AnnoDraw (~annotation draw), followed by Genodraw (~genome draw), and the current place-holder EMBL2image (The annotated sequence files are in 'EMBL format').
Does anyone have any better ideas?
I don't - but of those, I like Genodraw.
It also seems that in order to be successful that nowadays a project needs a good logo, ideally of a cute furry mascot. I'd quite like some sort of british-native animal, but I'm willing to be swayed from that. Any suggestions about this, or how to go about it? Not an animal, but given that the EMBL logo appears to be based around this basic design, and your sequence files are in EMBL format, the the basic shape (a hexagon) would be a good starting point (see the file I will hopefully attach to this in a mo) - perhaps as a containing shape for something else.
Possible things to put inside it might be a simple DNA strand (the basic shape that everyone, even Joe "Don't go in for book learning" Public, recognises) - I couldn't find a nice, clean (and most importantly royalty fee) example to try it with and see what it looked like.
Another possibility, given that it's web based would be to put a web inside the shape - I tried that (I drew a perfectly good web the other day to use as a starting point for new WebChange logos etc) but it looked awful. (Several variations, the web centred, centred on the bottom, slightly off centre - even based on the location of the red spot - but they all looked awful. Too busy, mainly.
(I don't have even 200 pounds to get these designed, the money I got for doing this was used up ages ago.) Sometimes inspiration can come unexpectedly - so you might suddenly have a brainwave, mention it here, and ten minutes later someone might come up with the goods. 
[Edited by VincceH at 22:54, 9/3/2007] |
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Tony Haines |
Message #99771, posted by Loris at 17:53, 11/3/2007, in reply to message #99702 |
Ha ha, me mine, mwahahahaha
Posts: 1025
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Not an animal, but given that the EMBL logo appears to be based around this basic design, and your sequence files are in EMBL format, the the basic shape (a hexagon) would be a good starting point (see the file I will hopefully attach to this in a mo) - perhaps as a containing shape for something else. mmm.
Possibly. Honestly, it doesn't grab me. Although its dot construction does remind me a little of the BBC computer owl.
Possible things to put inside it might be a simple DNA strand (the basic shape that everyone, even Joe "Don't go in for book learning" Public, recognises) - I couldn't find a nice, clean (and most importantly royalty fee) example to try it with and see what it looked like. The EBI site does the DNA inside thing, with dots.
Another possibility, given that it's web based would be to put a web inside the shape - I tried that (I drew a perfectly good web the other day to use as a starting point for new WebChange logos etc) but it looked awful. (Several variations, the web centred, centred on the bottom, slightly off centre - even based on the location of the red spot - but they all looked awful. Too busy, mainly. I think you've done quite well with that web-in-hexagon, given the starting material, but please don't brainstorm for ideas for the logo or name around EMBL territory.
There are several reasons to avoid it:
There lots of puns etc around there already (eg. trEMBL).
I've used EMBL format, but I may in future extend the program to also accept genbank format (which is quite similar, differing only to annoy me) - which is the larger, American sequence databank [1].
EMBL haven't had anything to do with my development, the funding I got was from the SGM
Sometimes inspiration can come unexpectedly - so you might suddenly have a brainwave, mention it here, and ten minutes later someone might come up with the goods.
You are right - those are probably the reasons I'm whittering on in here, to get it straight in my brain, and then get someone else to do the difficult bit.
I'll try and attach that picture I made before...
1 There are actually 3 sequence databases, which share data and convert it into their own flavours. But there doesn't seem to be a converter available on the web, which is stupid. |
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Phil Mellor |
Message #99774, posted by monkeyson2 at 18:01, 11/3/2007, in reply to message #99697 |
Please don't let them make me be a monkey butler
Posts: 12380
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I have been considering the badger for it. (-) TB connotations. (+) Harry Hill connotations. (+) stripey (-) monochrome.
I don't want to use an extinct or endangered animal. Also: badgerbadgerbadger...
Maybe an invertebrate? I'm fond of snails, spiders, woodlice, harvestmen, millipedes...
Here is a fantastic tool, but that logo is rather ... functional.
Maybe I'm being swayed too much by firefox and linux. The one thegman pointed to for Haiku os, on Drobe, seems rather elegant. Something in the same vein would be fine, I guess. I did once make a nice (IISSM) image for my wife's ebay selling, which had butterflies on it. It's not really a logo though, is it?
If there was an acronym for the name that would help, provided it wasn't one of those tortured ones. I wouldn't put too much emphasis on the EMBL part of it; the program will only ever be a tiny tool compared to the might of the EBI databases. Give us some key words, then. |
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Tony Haines |
Message #99790, posted by Loris at 18:58, 11/3/2007, in reply to message #99774 |
Ha ha, me mine, mwahahahaha
Posts: 1025
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I did once make a nice (IISSM) image for my wife's ebay selling, which had butterflies on it. It's not really a logo though, is it?
Well, it fit the specs (X*Y) .
If there was an acronym for the name that would help, provided it wasn't one of those tortured ones. Give us some key words, then.Um, oh, yes...:
DNA, [nucleotide] sequence, map
annotation, (feature, qualifier),
image, picture, diagram, flexible, adaptable
hierarchical, parameter, specification, scope, depiction ...
OK, so you need to know more about how my program works to use these.
Basically an annotated feature is formed from a feature-type, and one or more qualifiers (which carry additional information). For each feature, the type and qualifiers are tested to see if they match a list of 'scopes'. If any do, the defaults are overwritten by a list of parameter specifications. There is a hierarchy of scopes, such that the more 'narrow' the scope, the higher the priority. So a scope of 'gene' would overrule the default, but in turn be overruled if the scope gave the name of the gene.
Then I splat out the resultant feature 'depictions' to an image using ImageMagick.
I'll upload an example, and add to that list if I think of anything else. If you get close to something I might be able to finish it off - I see there would need to be a 'B' for badger  . |
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Tony Haines |
Message #100331, posted by Loris at 11:51, 20/3/2007, in reply to message #99790 |
Ha ha, me mine, mwahahahaha
Posts: 1025
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So .. no more suggestions then?
Regarding the name, that probably means I'll go with either Annodraw or Genodraw.
Regarding a logo... I'm almost stumped and going to jack it in in favour or writing the name like it is in annotations.
The other possibility (since the logo may actually be more of a header) would be to use a millipede which would be attempting to put the features into position using all its legs.
The big problem with the latter is that I think it may be rather hard to draw. I might post my attempts later. |
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richard cheng |
Message #100338, posted by richcheng at 13:13, 20/3/2007, in reply to message #100331 |
Posts: 655
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I don't like Annodraw. "Annotation" is a rather broad term, of which your app only covers a fairly specific area.
Genodraw sounds good, though. |
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Tony Haines |
Message #100392, posted by Loris at 23:47, 20/3/2007, in reply to message #100338 |
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Posts: 1025
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Thats a good point, damn. Just when I think one is getting ahead, the other one comes back.
Hmmm. Googlefight says :
Annodraw: 13 hits
Genodraw: 6 hits
This page is the top hit for both, then its random code labels and guff. So neither term is being used at the moment (which is not suprising, because I originally googled many proposals and rejected those already in use.)
It is true that 'annotation' is a general word, but within the domain of biology it is pretty exclusively used for annotated sequence data. Plus I guess for most annotations it doesn't make sense to talk of drawing them, which is part of the reason why the name hasn't been used already.
Genodraw just doesn't look as nice on the page.
I'll have to dither on this some more.
Still no logo, I might get some quality RISC OS rendering time on thursday.
Oh, and someone else said they liked an old idea of a frog mascot, which does have the advantage that I can draw something approximating a cartoon frog. |
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richard cheng |
Message #100406, posted by richcheng at 11:27, 21/3/2007, in reply to message #100392 |
Posts: 655
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It is true that 'annotation' is a general word, but within the domain of biology it is pretty exclusively used for annotated sequence data. Plus I guess for most annotations it doesn't make sense to talk of drawing them, which is part of the reason why the name hasn't been used already. I was thinking more of people who aren't involved in biology. Annodraw to me, sounds like an application that allows you to make drawings and then annotate them.
On the other hand, why would a non-biologist be looking at your program? Possibly my objection is a bit unfounded. |
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Tony Haines |
Message #100443, posted by Loris at 18:15, 21/3/2007, in reply to message #100406 |
Ha ha, me mine, mwahahahaha
Posts: 1025
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I was thinking more of people who aren't involved in biology. Annodraw to me, sounds like an application that allows you to make drawings and then annotate them. Well.. when you put it like that, I kind of agree.
My boss doesn't like Annodraw for a similar reason - he says it doesn't really describe what you're doing with it. Then he suggested 'MapDraw', which has ~14,300 hits on Google, or ~600 if you also search with 'DNA', 'sequence' or similar, and of course several programs with that name already exist. And I should go off and make a list of things it could be (which of course I already did).
For some reason he isn't swayed by Genodraw.
Anyway, he's thinking about it now, hopefully he'll have a good suggestion or two.
I'm very tempted by the millipede mascot idea, because they kind of look cute anyway:
http://www.swva.net/fred1st/millipede.jpg
http://coolcosmos.ipac.caltech.edu//image_galleries/ir_zoo/images/millipede_vis.jpg |
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Tony Haines |
Message #100491, posted by Loris at 14:37, 22/3/2007, in reply to message #100443 |
Ha ha, me mine, mwahahahaha
Posts: 1025
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So I've been waiting for my parents this morning, and this is the result (attached, hopefully).
None of them are satisfactory, but maybe they could be built on.
I really wanted to get a sense of urgent balancing and fitting in to place with the millipede, and clearly I'm nowhere near that.
We also had a brainstorm on the name, with the following possibilites:
genoscheme (0 google hits)
genescheme "
genotator (knicked already by some git for his annotating software)
genarranger (yeugh!)
gene ploterator (0 google)
dnapixie (dna pix is taken, & this is too close to it) |
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Jeffrey Lee |
Message #100492, posted by Phlamethrower at 14:40, 22/3/2007, in reply to message #100491 |
 Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot stuff
Posts: 15100
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genoscheme (0 google hits)
genescheme "
genotator (knicked already by some git for his annotating software)
genarranger (yeugh!)
gene ploterator (0 google)
dnapixie (dna pix is taken, & this is too close to it) geneonator?  |
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VinceH |
Message #100542, posted by VincceH at 19:01, 22/3/2007, in reply to message #100492 |
Lowering the tone since the dawn of time
Posts: 1600
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bionator? |
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Tony Haines |
Message #100546, posted by Loris at 19:32, 22/3/2007, in reply to message #100542 |
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Posts: 1025
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bionator? 44,000 hits on google, its some sort of denture, sorry.
Some more words/phrases which might help
Genome, gene, genetic map, sequence map,
plot, chart, plan, diagram <Oh, I had that>
Genome (the entire genetic sequence of an organism) is a good word to incorporate, I should have mentioned it before. Its the seminal word of a series of increasingly preposterous biological words (proteome, metabolome, interactome and so on). Oh, that reminds me of an old suggestion:
Drawnomics. |
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Jason Togneri |
Message #100550, posted by filecore at 20:12, 22/3/2007, in reply to message #100546 |
Posts: 3868
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http://www.rinkworks.com/namegen/ ? |
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Tony Haines |
Message #100791, posted by Loris at 15:55, 26/3/2007, in reply to message #100550 |
Ha ha, me mine, mwahahahaha
Posts: 1025
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http://www.rinkworks.com/namegen/ ? Um, wha?
NEW SUGGESTION by a colleague.
Genogator
I quite like this |
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richard cheng |
Message #100796, posted by richcheng at 16:58, 26/3/2007, in reply to message #100791 |
Posts: 655
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Also, you could have a CROCODILE as the logo. RAWR! |
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Ian Cook |
Message #100798, posted by ilcook at 17:25, 26/3/2007, in reply to message #100796 |
 Resident idiot
Posts: 1077
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Or better still an aligator, which would look snapy. |
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VinceH |
Message #100803, posted by VincceH at 19:05, 26/3/2007, in reply to message #100798 |
Lowering the tone since the dawn of time
Posts: 1600
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And you could call him Eugene. |
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richard cheng |
Message #100830, posted by richcheng at 09:34, 27/3/2007, in reply to message #100798 |
Posts: 655
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Or better still an aligator, which would look snapy. But wouldn't be as amusingly incongruous. |
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richard cheng |
Message #100831, posted by richcheng at 09:35, 27/3/2007, in reply to message #100803 |
Posts: 655
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And you could call him Eugene. You could call her Eugene. |
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VinceH |
Message #100835, posted by VincceH at 10:41, 27/3/2007, in reply to message #100831 |
Lowering the tone since the dawn of time
Posts: 1600
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And you could call him Eugene. You could call her Eugene.
Why would you want to do that if he's a masculine blokey aligator, and not a cissy girly one? You'll confuse the poor thing. |
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Tony Haines |
Message #100836, posted by Loris at 11:26, 27/3/2007, in reply to message #100835 |
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Posts: 1025
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And you could call him Eugene. You could call her Eugene.
Why would you want to do that if he's a masculine blokey aligator, and not a cissy girly one? You'll confuse the poor thing.
So I think we have a winner.
I'm going to use something like the attached as the logo. Its an ornament I bought in a charity shop. I'd do a redrawn version with the same colours, but I don't really have the skill for that.
Whether it is a crocodile or an alligator, male or female is for the viewer to decide. And it could be called Eugene, or possibly Snapy. |
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Richard Goodwin |
Message #100837, posted by rich at 12:42, 27/3/2007, in reply to message #100836 |
Dictator for life
Posts: 6828
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Quick and, indeed, dirty:
________
Cheers,
Rich.
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Jeffrey Lee |
Message #100838, posted by Phlamethrower at 13:01, 27/3/2007, in reply to message #100837 |
Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot Hot stuff
Posts: 15100
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Somehow, I knew you were going to have a go at doing a logo |
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richard cheng |
Message #100844, posted by richcheng at 13:35, 27/3/2007, in reply to message #100838 |
Posts: 655
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Needs fangs. |
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