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Linux Applications for another failure

Well, It is not a choice. I have to work on Linux platform since I joined a part time job at biotech gene annotation lab. Now,the website was settled and development is done. The researcher told me to analyze DNA sequence datasets and blah blah…

So,Ubuntu becomes my home because most of bioinformatics tool are Linux binary applications. Let’s say around 6 months, this Linux distro fails me 3 times. Even though it said “Ubuntu 12.04 LTS(Long Term Support)”. You should call it as “Long Time to Stable”.

Anyway,I have to use it and I try to find the best applications. Here is the list for next Ubuntu installation after boot failure.


  1. Clementine: music player with lots of features
  2. Nuvola player: online music players for services such as 8tracks,Deezer,Rdio …
  3. last.fm- last.fm scrobbling client
  4. Miro- online video player
  5. VLC player- media player
  6. RadioTray- light-weight online radio player
  7. Puddletag - Music Tag editor
  8. Mustique- iTunes like light-weight beautiful music player
  9. Minitube- Youtube Desktop player


  1. Chrome & Chrominium- browser
  2. Polly- Twitter Client
  3. Deluge- Bittorrent Client
  4. Dropbox - Dropbox Client
  5. InSync- GDrive Client
  6. Everpad- Evernote Client
  7. Skype - Video Conferencing app
  8. Teamviewer - PC Remote tool
  9. Viber- Viber for PC(still in development and it sucks)
  10. Wireshark - Network analysis tool
  11. Filezilla- FTP Client
  12. Pidgin- Instant Messenger

Development Tools

  1. SublimeText- text editor
  2. Bracket- another text editor from adobe
  3. LightTable- Revolutionary text editor (still in development)
  4. Eclipse- multi-language iDE
  5. Emacs & Vim- father of sublime text
  6. Retext & UberWriter- Markdown editor
  7. SmartGit- GUI Git Client
  8. SmartSynchronize- File Merge tool
  9. Dia- Diagramming tool
  10. Gitblit- Tool to deploy local Git server
  11. Putty- Telenet/SSH client


  1. Libre Office Suite
  2. Evolution- Mail Client(setup in pain in the ass)
  3. Geary- Another light-weight Mail Client(suck!!)

Graphics & Reader

  1. Comix- comic reader(cbz,crt..)
  2. qcomicbook- another comic reader
  3. chmSee- .chm format reader
  4. Adobe Pdf- Pdf reader
  5. Scribus- DTP tool
  6. shotwell- photo viewer
  7. GIMP- Image editor

Utility & Tweak tools

  1. Htop- command-based task monitoring tool
  2. Synaptic Package Manager- Application Package manager
  3. Conky Manager- Manager for Conky
  4. Bumblebee- tools to manage optimus-based hybrid graphic driver
  5. Deepin Software Center- Alternative software center
  6. Caffine- tool to temporarily prevent the activation of both the screen saver and the sleep mode
  7. F.lux - tool to change monitor lighting based on location and time
  8. Jupiter- Power Management tool
  9. dconf Editor- Low level system configuration manager
  10. Y PPA Manager- GUI PPA manager
  11. Variety- automatic wallpaper changer
  12. Cariodock- Desktop Docker
  13. Terminology- Best terminal emulator
  14. bpipe- Script pipeline manager
  15. dphys-swapfile- automatic swapfile manager
  16. Natural Scrolling- Mac Like natural scrolling supports for touchpad and mouse
  17. Ubuntu-Tweak- various tweak tool for Ubuntu
  18. Bleachbit- System Cleaner
  19. Gloobus Preview- Mac Like instant file viewer
  20. Synapse- Universal Search tool in one click away
  21. PlayonLinux- front-end tool for Wine, Windows env emulator
  22. Oracle VM- Virtual Box

Themes & Grooming tools

  1. Numix- favourite GTK Theme
  2. Moka- best icon theme with daily update
  3. Moka- companion window theme of Moka
  4. CompizConfigSettingManager(CCSM)- desktop animation tweak tool for high-end machine

Yeah..I know.It’s exhausting. Who said Linux platform lacks of application? You just need to look for it.

This post is licensed under CC BY 4.0 by the author.


DNA Sequencing pipeline for 454 GS/FLX runs