Some tips on Unix and Bioinformatics. 'T' is for 'Text editors', 'Time', and 'Tab-completion' This was a talk given at UC Davis on 15th June 2015 as part of a Bioinformatics Core teaching workshop. Author: Keith Bradnam, Genome Center, UC Davis. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

1. Today's bioinformatics lesson
is brought to you by the letter 'T'
by
Keith Bradnam
Today'sbloinformatieslesson
isbroughttoyoubytheletterT1

2. T
is for Text editorsisforTexteditors

3. There are many Unix text editors!TherearemanyUnixtexteditors!

4. Editors Super powers Learning curve
Nano None Shallow
Emacs All of them Very steep
Vi All of them Very steep
Vim All of them Very steep
Editors SuperpowersLearning curve
Nano
Emacs
Ali
Vim
None Shallow
Allofthem V e r y steep
Allofthem V e r y steep
Allofthem V e r y steep

5. These editors are available on
every Unix system from the terminal
Theseeditorsareavailableon
everyUnixsystemfromtheterminal

6. https://en.wikipedia.org/wiki/Comparison_of_text_editorshttps://en.wikipediaorgiwiki/Comparisonoftexteditors

7. Texteditorsupportforvariousoperatingsystems
416 Windows t 1OSX * Linu BSD * Unix 0penVMS*
Acme Yes Yes Yes Yes Yes No
AkelPad Yes N o N o N o N o N o
Mphatk Yes Yes Yes Yes Yes Yes
Aquamacs No Yes No N o No No
Yes Yes Partiailli • No N oAtom
Arachnophilla Yes Y e s Yes Yes Yes N o
BBEdit No Y e s N o N o N o N o
Bluefish Yes1 Yes Yes Yes Yes Yes
Brackets Yes Yes Yes N o No No
Coda No Y e s No N o N o N o
ConTEXT Yes No No N o N o N o
CrimsonEditor Yes No N o N o N o N o
Diakonos Yes Y e s Y e s Yes Yes No
ed Yes Y e s Y e s Yes Yes Yes
EditPlus Yes N o No N o N o N o
Editra Yes Y e s Yes
EmEditor Yes N o N o N o N o No
epsilon Yes Y e s Y e s Y e s N o
Yes!Yes Yes Y e s Y e sGeany Yes Yes
gedit Yes Ye s [ 3 ] Ye s Y e s Y e s N o
GNUEmacs Yes Y e s Y e s Y e s Y e s Y e s
Gobby Yes Y e s Y e s Y e s Yes No
JED Yes Yes Y e s Y e s Yes Yes
'Edit Yes Yes Y e s Y e s Yes No
JOE Partialm Yes Yes Y e s Yes No
JOVE Yes Y e s Yes Yes Yes No
Kate Partial[5] Yes Yes Yes Yes No
KEDIT Yes No Yes Yes No No
Kod No Yes No No No No
•

8. Programmingfeatures[edit]
, hi
Acme
AkelPad
Alphatk
Aquamacs
BBEdit
Bluefish
Brackets
Coda
ConTEXT
CrimsonEditor
Yes
Yes
Yes
Yes
Diakonos
Yes
ETextEditor
Yes
ed
Yes
EditPlus
Editra
EmEditor
No
Geany
No
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
gedit
Yes
GNUEmacs
Gobby
Yes
JED
jEdlt
JOE
Yes
JOVE
Kate
KEDIT 1M
Brace
matching
Auto
indentation
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Plug-in
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
No • No
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
•
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes Yeses
Syntax
ghlighting
No
Plug-in
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
No
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
No
Yes
Yes
Function
list
Yes
Plug-in
Yes
Yes
No
Yes
Yes
No
No
No
Yes
Plug-in
Plug-in
Texteditorsupportforprogrammingfeatures(seesourcecodeeditor)
Symbol
database
(ctagsorequiv.)
Yes
Yes
No
Yes
Partial(45)
Partial
M r N7—.1
Pat a05)
Plug-in
Yes[49)
Plug-in
Yes
No
Yes
Yes
Plug-in
Macro
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Auto
completion
Yes
Plug-in
Yes
E N o I
• N o
Yes[471
Plug-in1481
Yes
Plug-in
Yes
No
Yes
Yes
• N o I
Yes
• N o
Code
folding
• N o
Poug-n
Yes
Yes
Yes
Yes
Yes
Yes
No
No
• N o
Yes
• N o
Yes
Yes
Yes
Partial
No
Yes
• N o
Yes
Yes
No
No
Yes
Yes
Text
folding
No
No
Yes
Yes
Yes
No
Yes
No
No INo
No
Yes
No
No
Yes
No
Plug-in(50
Yes
No
Yes
Yes
No
No
Yes
Yes
Compiler
Integration
Yes
Plug-in
Yes
Yes
Yes
Yes1441
Plug-in
No
Yes
Yes
No
Yes
No
Yes
Yes
Yes
Yes[51I
Yes
• No
Yes
Plug-in
Yes
Yes
Plug-in
Yes

9. T
is for TimeisforTime

11. It takes time to learn command-line skillsIttakestimetolearncommandlineskills

12. But those skills will always remain useful!Butthoseskillswillalwaysremainuseful!

13. Future usefulness of various skills
Windows 10
skills
Bioinformatics
programs
Unix
commands
Today
1 year from now
5 years from now
?
10 years from now
X ?
20 years from now
X X
Futureusefulnessofvariousskills
Windows10
skills
Bloinformatics U n i x
programscommands
Today
1yearfromnow
5yearsfromnow
10yearsfromnow
20yearsfromnow
t t t
X ? i f

14. Keep learning!Keeplearning!

15. T
is for Tab-completionisforTab-completion

16. esc
0,0
1
1
„
2
option
w1
I:230 17:7
3
F
•••••
command
ODD
ODDF4
4 5
A
6
&
7
44
8
)11
1
9
•••:
:ommand option
ril
1
4))) F12
A
delete

17. Tab-completion is your friendTab-completionisyourfriend

18. Tab-completion will probably save you more
time than anything else you will learn
Tab-completionwillprobablysaveyoumore
timethananythingelseyouwilllearn

19. The endTheend