User:Squidonius

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User is currently fighting his wiki-addiction, sorry
some images for clip art.. left here for now
some images for clip art.. left here for now

Image text issue: I apologise for some images having a font issue (arialMT) I have fixed some manually, but I need to figure out how to save the fonts as paths automatically in inkscape (help welcome).

Contents

[edit] Stuff

[edit] Data mining NCBI and Wikipedia with Perl

[edit] Wikipedia

[edit] NCBI

  • my $esearch = "$utils/esearch.fcgi?db=$db&retmax=1&usehistory=y&term=$query";
  • my $esearch_result = get($esearch);
  • $esearch_result =~ m|<Count>(\d+)</Count>.*<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>|s;
  • my $efetch = "$utils/efetch.fcgi?rettype=$report&retmode=text&retstart=$retstart&retmax=$retmax&" ."db=$db&query_key=$2&WebEnv=$3";
  • my $efetch_result = get($efetch);

[edit] Notes

  1. by taxonID is a strage one $query = "txid"."$array[$i]"."[Organism:noexp] AND $smelly_protein"
  2. Taxon ID number is "uilist";
  3. wikispecies used tempates and stuff, but that is not a problem (template:malacostraca) although produces "interesting" results...

[edit] bioinformatics, Windows and Linux

Most software is webbased but if one wanted to run a linux software (check first, Linux and recently Mac are Unix based) on a windows PC you can either install a Linux distro, such as KDE 4.0 (personally nicer graphics but a bit more start up work) or Ubuntu (doable ever for the less savy). Alternatively often it is only one program so cygwin might be better (such as on shared PC) (although switching to Linux is the best option if you can handle a computer moderately well).

here is the how:

  1. Download cygwin, a linux emulator-ish for windows (site:[1] download:[2])
  2. Choose appropriate mirror site to download it (.org = UK, .com = US, .de etc)
  3. on installation options screen press the circle arrow button next to all from default to all
  4. make a cup of tea
  5. press the icon on the desktop and it will load a (command line interface=MS-Dos style) shell called bash: some commands are similar to dos "cd" and "dir", mess around freely (you cannot delete windows to do that you must boot the pc with a liveCD), to find out about a command just add --help to it.
  6. optional: change the icon to a penguin icon!
  7. download program that is wanted for example MEME a sequence motif detection program. (site:[3] download: [4]) .tar is a tarball, a unix file extension and it is compressed with gunzip. WinRar can open it, if not you can extract it with cygwin's gunzip.
  8. rember where you extracted it to. run cynwin and get to the folder: cd c:/users/Squidonius/Desktop/Meme (my wikipedia username is just an example)
  9. type ./configure
  10. if all goes well, it should give you three options which should be done in order: install (make setup) check the installation (make test) and something else.
  11. meme is installed somewhere, probably c:/cygwin/home/Squidonius/bin go there!
  12. ./meme c:/users/Squidonius/Desktop/hsp70.fasta -protein >hsp70.html argument list can be found on the manual [5]
  13. Many Linux distros have nice graphics (better than Mac!), like Ubuntu, which is easier to install than windows, many times more userfriendly than windows, and better graphics and easy to make an uber-pownage mean machine. Although having a dual boot computer has some implications (windows cannot read linux partitions), it is not terribly drastic.


"My clipborad"

[edit] Desparte needs

  • better organization of regulation pages
  • fix a concept pages Autoregulatory loop etc
  • Cell signalling... small molecule inhibitors are ligands too
  • methods and tools


[edit] cleanup tag, a copy and paste thing for my use

This article has had a Cleanup tag for a lengthy amount of time and no discussion is present discussion what is requested for the tag. which is just a general tag more precise tags can be found here [6].
It may be due to bad grammar {{grammar}}
It may be due too long {{verylong}}
It may be due to bad information {{Expert-verify}}
It may be due to old content {{update}}
It may be due to confusing content {{cleanup-confusing}}
It may need to be wikified {{wikify}}

[edit] New template for talk pages, expecially the larger ones

Unanswered query This question or request has not been resolved
Remove this tag when this is resolved.

Some pages, such as this one have lots of post, and it requires some work to see what has been answered or acknowledged. therefore I have helped make the {{Unanswered}} template that can be put above a section allowing one to quickly glimpse what has been answered. If you were waiting for an answer but never got one as the post in somewhere in the middle tag it! please voice any queries or comments in the talk page ofTemplate:Unanswered (links, talk) and not here. Cheers --Squidonius (talk) 15:12, 13 April 2008 (UTC)

[edit] Cool molecular biology facts

A list of interesting pages, might make some thing useful one day with it..