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| ==Protocols== | | ==Protocols== |
- | *[[Molecular biology]]
| + | ;[[Molecular biology]] |
- | *[[Protein biochemistry]]
| + | |
- | *[[Chemistry]]
| + | |
| | | |
- | ==Part list==
| + | ;[[Protein biochemistry]] |
- | *[[Plasmids]]
| + | |
- | *[[Strains]]
| + | |
- | *[[Parts Registry]]
| + | |
| | | |
- | ==X-ray crystallography==
| + | ;[[Chemistry]] |
- | *Related programs are installed at [[panflam]] (linux machine; 2 CPU (8 cores))
| + | |
- | <pre>/home/x-ray</pre>
| + | |
- | *Environment Setup (for <i>tcsh shell</i>) - panflam
| + | |
- | *Check your login SHELL
| + | |
- | <pre>
| + | |
- | echo $SHELL
| + | |
- | /bin/tcsh # you should see this if you use 'tcsh'
| + | |
- | </pre>
| + | |
- | *then, modify your shell enivironment - add followings into ''.cshrc'' file in your home directory
| + | |
- | <pre>
| + | |
- | # x-ray setting
| + | |
- | setenv XRAY /home/x-ray
| + | |
- | ## CNS
| + | |
- | source $XRAY/cns_solve_1.2/cns_solve_env
| + | |
- | ## phenix
| + | |
- | source $XRAY/phenix-1.5-2/phenix_env
| + | |
- | ## ccp4
| + | |
- | source $XRAY/setup-scripts/csh/ccp4.setup
| + | |
- | source $XRAY/setup-scripts/csh/ccp4-others.setup
| + | |
- | </pre>
| + | |
- | *activate the enivronment
| + | |
- | <pre>
| + | |
- | source ~/.cshrc
| + | |
- | </pre>
| + | |
- | *[[panpyro]] - cluster
| + | |
- | <pre>
| + | |
- | # x-ray
| + | |
- | # phenix 11-07-2009
| + | |
- | source /home/x-ray/phenix-1.5.2/phenix-1.5-2/phenix_env
| + | |
- | # ccp4
| + | |
- | source /home/x-ray/ccp4/setup-scripts/csh/ccp4.setup
| + | |
- | source /home/x-ray/ccp4/setup-scripts/csh/ccp4-others.setup
| + | |
- | </pre>
| + | |
- | *running ''phenix'' by 'qsub' on multiple processers [[panpyro]]
| + | |
- | *<b>EXAMPLE</b>
| + | |
- | <pre>
| + | |
- | # swissmodel superimposed to 1V19 MR solution
| + | |
- | phenix.autobuild ../MR.1_copy.mtz ../swissAB.pdb seq_file=../sde2656.fas run_command="qsub -q infi" background=False nproc=5 nbatch=5 >& job.log &
| + | |
- | phenix.automr ../pointless_sde2656_1_001_scala1-2.6A.mtz ../MR2_1V19_polyALA.pdb seq_file=../sde2656.fas copies=2 identity=25 run_command="qsub -q infi" background=False nproc=5 nbatch=5 >& job.log &
| + | |
- | </pre>
| + | |
| | | |
- | *[[X-ray programs]]
| + | ==CSBL Part list== |
- | *Methods
| + | ;[[Plasmids]] |
- | **[[Molecular replacement]]
| + | |
| + | ;[[Strains]] |
| + | |
| + | ;[[Parts Registry]] |
| + | |
| + | ==[[X-ray programs|X-ray Software@CSBL]]== |
| + | ;Installed at panflam and panpyro (cluster) |
| | | |
| ==Computing resources== | | ==Computing resources== |
- | #[[Compbio]]
| + | ;[[Compbio]] |
- | #[[Microbio]]
| + | |
- | #[[Panpyro]]
| + | ;[[Microbio]] |
- | #[[Panflam]]
| + | |
| + | ;[[Panpyro]] |
| + | |
| + | ;[[Panflam]] |
| | | |
| ==Unix & Programming== | | ==Unix & Programming== |
- | ===Unix=== | + | ===[[Unix]]=== |
- | *[https://help.ubuntu.com/community/InstallingCompilers Installing Compilers]
| + | ===[[Web]]=== |
- | *[[SSH]] - how to connect the Lab. PC from your home
| + | ===[[Python]]=== |
- | *X11 connection
| + | ;[http://biohackers.net/wiki/BioPythonStudy BioHacksNet - 한글번역] |
- | **Easy safe way is to use SSH's X forwarding:
| + | |
- | <pre>ssh -X me@remotemachine</pre>
| + | |
- | *check ''ssh_config & sshd_config'' (/etc/ssh/) by [http://www.ssh.com/support/documentation/online/ssh/adminguide/32/X11_Forwarding.html SSH]
| + | |
- | <pre>X11Forward yes</pre>
| + | |
- | *<b>''old way - no need to follow''</b>
| + | |
- | Your display will look to the remote machine like:
| + | |
- | <pre>echo $DISPLAY
| + | |
- | localhost:10.0
| + | |
- | firefox --display=$DISPLAY &
| + | |
- | </pre>
| + | |
- | ''xhost/export DISPLAY''
| + | |
- | *On your local machine:
| + | |
- | <pre>xhost + remotemachine</pre>
| + | |
- | *On the remote machine:
| + | |
- | <pre>export DISPLAY=localhost:0.0</pre>
| + | |
- | *After you're done, remove remote machine access from your xhost:
| + | |
- | <pre>xhost -</pre>
| + | |
| | | |
- | *SCIM - [http://www.ubuntu.or.kr Input Hangul]
| + | ;[http://openwetware.org/wiki/BE.180 BE.180 Biological Engineering Programming] - Synthetic biology@MIT Check "Unix&Python" tutorials! |
- | *Linux (Unix) [http://hancoma.springnote.com/pages/621424.xhtml commands]
| + | :[[Media:python_sheet.pdf|Python Cheat Sheet]] |
- | *[http://tldp.org/ The Linux Document Projects] - Numerous useful documents & tutorials are available
| + | :[[Media:unxpython_tut_06.pdf|Unix&Python tutorial]] |
- | *Change locale (language) for 'panpyro'
| + | |
- | <pre>bash shell:
| + | |
- | export LC_ALL=en_GB.ISO8859-1
| + | |
- | export LANG=en_GB.ISO8859-1
| + | |
- | </pre>
| + | |
| | | |
- | ===Python===
| + | ;[http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/ Pycluster]: Open source Clustering software |
- | *[http://openwetware.org/wiki/BE.180 BE.180 Biological Engineering Programming] - Synthetic biology@MIT Check "Unix&Python" tutorials!
| + | |
- | **[[Media:python_sheet.pdf|Python Cheat Sheet]]
| + | ;Tip |
- | **[[Media:unxpython_tut_06.pdf|Unix&Python tutorial]]
| + | :[http://adnoctum.tistory.com/500 Drag&Drop] |
| | | |
| ===Applications=== | | ===Applications=== |
- | *[[MySQL|MySQL]]
| + | ;[[MySQL|MySQL]] |
- | *[[Matlab|Matlab]]
| + | |
- | *[[R|R-project]]
| + | |
- | ----
| + | |
- | *[http://www.redbrick.dcu.ie/~noel/ECwheel.html Hypergraph: EC class]
| + | |
| | | |
- | ==Computing resources==
| + | ;[[Matlab|Matlab]] |
- | #[[Compbio]]
| + | |
- | #[[Microbio]]
| + | |
- | #[[Panpyro]]
| + | |
- | #[[Panflam]]
| + | |
| | | |
- | ==Unix & Programming==
| + | ;[[R|R-project]] |
- | ===Unix===
| + | |
- | *[https://help.ubuntu.com/community/InstallingCompilers Installing Compilers]
| + | |
- | *[[SSH]] - how to connect the Lab. PC from your home
| + | |
- | *X11 connection
| + | |
- | **Easy safe way is to use SSH's X forwarding:
| + | |
- | <pre>ssh -X me@remotemachine</pre>
| + | |
- | *check ''ssh_config & sshd_config'' (/etc/ssh/) by [http://www.ssh.com/support/documentation/online/ssh/adminguide/32/X11_Forwarding.html SSH]
| + | |
- | <pre>X11Forward yes</pre>
| + | |
- | *<b>''old way - no need to follow''</b>
| + | |
- | Your display will look to the remote machine like:
| + | |
- | <pre>echo $DISPLAY
| + | |
- | localhost:10.0
| + | |
- | firefox --display=$DISPLAY &
| + | |
- | </pre>
| + | |
- | ''xhost/export DISPLAY''
| + | |
- | *On your local machine:
| + | |
- | <pre>xhost + remotemachine</pre>
| + | |
- | *On the remote machine:
| + | |
- | <pre>export DISPLAY=localhost:0.0</pre>
| + | |
- | *After you're done, remove remote machine access from your xhost:
| + | |
- | <pre>xhost -</pre>
| + | |
| | | |
- | *SCIM - [http://www.ubuntu.or.kr Input Hangul]
| + | ;[http://www.redbrick.dcu.ie/~noel/ECwheel.html Hypergraph: EC class] |
- | *Linux (Unix) [http://hancoma.springnote.com/pages/621424.xhtml commands]
| + | |
- | *[http://tldp.org/ The Linux Document Projects] - Numerous useful documents & tutorials are available
| + | |
- | *Change locale (language) for 'panpyro'
| + | |
- | <pre>bash shell:
| + | |
- | export LC_ALL=en_GB.ISO8859-1
| + | |
- | export LANG=en_GB.ISO8859-1
| + | |
- | </pre>
| + | |
| | | |
- | ===Python===
| + | ;[http://en.wikipedia.org/wiki/Social_network_analysis_software SNA softwares] |
- | *[http://openwetware.org/wiki/BE.180 BE.180 Biological Engineering Programming] - Synthetic biology@MIT Check "Unix&Python" tutorials!
| + | |
- | **[[Media:python_sheet.pdf|Python Cheat Sheet]]
| + | |
- | **[[Media:unxpython_tut_06.pdf|Unix&Python tutorial]]
| + | |
| | | |
- | ===Applications=== | + | === mediawiki === |
- | *[[MySQL|MySQL]]
| + | ;[http://www.mediawiki.org/wiki/Manual:Extensions/ko Extension] |
- | *[[Matlab|Matlab]]
| + | |
- | *[[R|R-project]]
| + | |
- | ----
| + | |
- | *[http://www.redbrick.dcu.ie/~noel/ECwheel.html Hypergraph: EC class]
| + | |
| | | |
| ==Windows== | | ==Windows== |
- | *MS-Word - [http://office.microsoft.com/ko-kr/word/HA012186901042.aspx 편집시 변경내용 추적]
| + | ;MS-Word - [http://office.microsoft.com/ko-kr/word/HA012186901042.aspx 편집시 변경내용 추적] |
| + | |
| + | ==[[Reading, Writing and Speaking|Reading, Writing and Speaking]]== |