Wiki CEINGE - New pages [en]

CV-DISEASE

Angelo — Sat, 08 Jan 2011 12:52:11 GMT

Summary:

In preparation.

Access to data is currently limited to authorized users. If you have access, please click [http://mac-web.ceinge.unina.it/cvdis/ here].

{{footer resdbs}}

CARDIODISEASE

Angelo — Fri, 07 Jan 2011 12:28:05 GMT

Summary:

Documentation not yet available

Bioinfolocal:BiodevProjectInit

Angelo — Wed, 14 Oct 2009 10:43:53 GMT

Summary: New page: On clr55, as root cd to /biodev/.projects/admin/ enter a command such as ./initprj.php -p motocell -m francesca,concita,angelo where with '''-p''' is defined the '''project name''' an...

On clr55, as root
cd to /biodev/.projects/admin/

enter a command such as
./initprj.php -p motocell -m francesca,concita,angelo

where with '''-p''' is defined the '''project name'''

and with '''-m''' is specified the comma-separated list of system users authorized to access and modify the project files

Linux raid

Gianluca — Thu, 19 Jun 2008 09:24:46 GMT

Summary: New page: Verify raid status: <pre> mdadm --detail /dev/md0 </pre>

Verify raid status:

<pre>
mdadm --detail /dev/md0
</pre>

Smb ceinge for Apple MacOSX

Gianluca — Wed, 27 Feb 2008 15:19:32 GMT

Summary:

Mac OSX supports the smb protocol to access Ms Windows shares, using its embedded standard way to connect to remote volumes.

Using the Finder menu, select "Go" and "Connect to..." entries:

[[Image:smbOSXconnect.jpg]]

Insert the server name:

[[Image:smbOSXset.jpg]]

Select the needed shared volume:

[[Image:smbOSXvolumes.jpg]]

Fill in the authentication parameters with your username and password:

[[Image:smbOSXauth.jpg]]

Access the volume content:

[[Image:smbOSXcontent.jpg]]

{{footer|footername=footer main}}

SmbFSwXP

Gianluca — Wed, 27 Feb 2008 14:24:48 GMT

Summary:

Windows XP supports natively the mount of shared volumes by using smb protocol. Go in the Network window selecting the correct entry in the "Start" menu and click on the Search button to enter the ceinge server name:

[[Image:smbWinxpSearch.jpg]]

Once the server is found, double click on it and fill the authentication dialog box with your username and password.

The volumes appear:

[[Image:smbWinxpVolumes.jpg]]

Choose your volume and use the content:

[[Image:smbWinxpHome.jpg]]

{{footer|footername=footer main}}

SmbFSLinux

Gianluca — Wed, 27 Feb 2008 11:29:21 GMT

Summary:

The smb protocol for Microsoft networking is fully supported in Linux environment and can easily be managed by using GUI and command line facilities and tools.

Please, choose your most suitable instructions:
* [[SmbFSLinux#KDE users|KDE users]]
* [[SmbFSLinux#GNOME users|GNOME users]]
* [[SmbFSLinux#Command line|Command line]]

== KDE users ==
The KDE desktop allow the use of the smb protocol to access the Microsoft Networking by using any kwin window:

[[Image:kwinsmb.jpg]]

Please note the syntax used to make the address:
<pre>
smb://username@smb.ceinge.unina.it
</pre>

Select the needed volume and authenticate:

[[Image:smbkwinauth.jpg]]

Done!

[[Image:smbkwinhome.jpg]]

== GNOME users ==
Gnome users can mount a shared MSwindows volume onto the desktop, following some easy steps:

[[Image:gnomesmbconnto.jpg]]

Set the basic info for the needed share:

[[Image:gnomesmbset.jpg]]

Done! The Volume icon appears on the desktop and a window shows the content:

[[Image:gnomesmbmount.jpg]]

== Command line ==
The Microsoft Networking can also be managed by command line, using the smbclient tool.

To browse the shares on the smb fileserver use:
<pre>
> smbclient -L smb.ceinge.unina.it -U%

Domain=[CEINGE] OS=[Unix] Server=[Samba 3.0.28-0.fc7]

Sharename Type Comment
--------- ---- -------
homes Disk Direct user Home
Home Disk All ceinge user Homes
FileServer Disk Ceinge software repository
Scratch Disk Ceinge scratch space
pastoreop Disk Pastore group
IPC$ IPC IPC Service (Ceinge file server)
</pre>

To enter the smb fileserver use the following command and authenticate as required:
<pre>
> smbclient -U busiello //smb.ceinge.unina.it/Home
Password:
Domain=[CEINGE-FILESERVER] OS=[Unix] Server=[Samba 3.0.28-0.fc7]
smb: \> cd busiello
smb: \busiello\> ls
. D 0 Wed Feb 27 12:06:29 2008
.. D 0 Thu Feb 21 15:55:38 2008
Public D 0 Tue Oct 9 17:19:32 2007
Sites D 0 Thu Apr 12 11:12:48 2007
Desktop D 0 Mon Apr 11 15:39:23 2005
login D 0 Fri Feb 22 15:46:21 2008
Pictures D 0 Mon Nov 19 18:02:12 2007
Library D 0 Tue May 20 16:24:33 2003
Bioinfo D 0 Mon Jan 3 18:27:14 2005
Documents D 0 Fri Feb 22 18:47:29 2008
Music D 0 Wed Feb 15 10:41:03 2006
Movies D 0 Tue Feb 26 16:32:38 2008
40960 blocks of size 131072. 22775 blocks available
smb: \busiello\>
</pre>

{{footer|footername=footer main}}

StoragePartitions

Gianluca — Mon, 18 Feb 2008 10:57:10 GMT

Summary: New page: Everyone is invited to discuss this page. Thanks

Everyone is invited to discuss this page.
Thanks

Bioinfolocal:veil

Gianluca — Fri, 15 Feb 2008 10:26:29 GMT

Summary: [[Bioinfolocal:veil]] moved to [[biolocal:Veil]]: moving to the right namespace

Veil is a shared postgres library, used to introduce complex access control onto the DB.

To install Veil on a RedHat based ditribution, be sure to have the devel package of your postgres installation:
<pre>
yum update postgresql-devel
</pre>

The base postgres RPMs will be installed in the following paths:

<pre>
pgconfigdir=/var/lib/pgsql/data
pgbindir=/usr/bin
pgincludedir=/usr/include/pgsql
pglibdir=/usr/lib
pgsharedir=/usr/share
</pre>

Download the Veil packet:
<pre>
wget http://pgfoundry.org/frs/download.php/1601/Veil-0.9.6.tar.gz
</pre>

Compile and install it:
<pre>
cd /usr/local/src
tar xvzf /downloadpath/Veil-0.9.6.tar.gz
cd Veil-0.9.6
./configure --prefix=/usr --with-pgconfigdir=/var/lib/pgsql/data --with-pgbindir=/usr/bin \ --with-pgincludedir=/usr/include/pgsql --with-pglibdir=/usr/lib --with-pgsharedir=/usr/share
make
make install
</pre>

Configure postgres server to load the new shared object:
<pre>
vi /var/lib/pgsql/data/postgresql.conf
</pre>

look for the shared_libriries directive and add the following:
<pre>
shared_preload_libraries = 'veil.so'
</pre>

Restart the postgres server.

For other OSs or postgres installation not based on binary packets, the procedure is very similar; just pay attention to set the correct postgres paths in the configure command.

Bioinfolocal:storagePartitions

Gianluca — Thu, 14 Feb 2008 12:43:25 GMT

Summary:

'''All the storage volumes:'''

{| border="1" cellspacing="0" cellpadding="5" align="center"
! Name
! Sys name (storage proc)
! Size
! Description
! Data type
! Disk type
! RAID type
! Host FC (read only/write)
! Host iSCSI (read only/write)
! Notes

|-
| bioinfo_hs
| data01 (spB)
| 2.6Tb
| high speed access to data used by bionformatic tools
|
*indexes
*flat files
*row data
| FC
| 5
|
*storagesrv1(rw)
*storagesrv2(rw)
*opa(rw)
*bpe(ro)
*G5(rw)
|
*cluster(rw)
|
|-

|-
| sql
| data02 (spA)
| 1,8Tb
| data for RDBMS
| backend files for relational DB servers
| FC
| 5
| opb(rw)
|
|
|-

|-
| bioinfo
| data03 (spA)
| 5,4Tb
| data for bionformatic tools
|
*flat files
*row data
| SATA
| 5
|
*storagesrv1(rw)
*storagesrv2(rw)
*opa(rw)
*bpe(ro)
*G5(rw)
|
*grid002(ro)
*cluster(rw)
| This is a superset of the bioinfo_hs volume, containing data not frequently accessed.
|-

|-
| images
| data04(spA)
| 5,4Tb
| data for imaging in biomedical research
|
*compressed images
*row images
| SATA
| 5
|
*G5(rw)
|
*cluster(rw)
*pc-bioinfo2(rw)
|
|-

|-
| mirrors
| data05 (spB)
| 2,6Tb
| external downloaded data
|
*compressed files
*row data
| SATA
| 5
|
*opa(rw)
*opb(ro)
|
|
|-

|-
| development
| data06 (spB)
| 5,4Tb
| data for development
| all
| SATA
| 5
|
*bpe(ro)
*G5(rw)
|
*cluster(rw)
|
|-

|-
| sqlexternal
| data07 (spA)
| 5,4Tb
| backend files for external relational DBs
| backend data for RDBMS
| SATA
| 5
|
*opb(rw)
|
|
|-

|-
| backup
| data08
| 5,4Tb
| local copies of sensible data
| all
| SATA
| 5
|
*opa(rw)
*opb(rw)
*G5(rw)
|
|
|-

|-
| diskless
| rootOSes,snapOSes
| 5,4Tb
| OS images and snapshots for diskless computers
| all
| SATA
| 5
|
*storagesrv1(rw)
*storagesrv2(rw)
|
|
|-

|}

'''The storage volumes available to the GRID'''
{| border="1" cellspacing="0" cellpadding="5" align="center"
! Name
! Sys name
! Size
! Description
! Data type
! Disk type
! RAID type
! Host FC (read only/write)
! Host iSCSI (read only/write)
! Notes

|-
| bioinfo_hs
| data01 (spB)
| 2,6Tb
| high speed access to data used by bionformatic tools
|
*indexes
*flat files
*row data
| FC
| 5
|
*storagesrv1(rw)
*storagesrv2(rw)
*opa(rw)
*bpe(ro)
|
*cluster(rw)
|
|-

|-
| bioinfo
| data03 (spA)
| 5,4Tb
| data for bionformatic tools
|
*flat files
*row data
| SATA
| 5
|
*storagesrv1(rw)
*storagesrv2(rw)
*opa(rw)
*bpe(ro)
|
*cluster(rw)
| This is a superset of the bioinfo_hs volume, containing data not frequently accessed.
|-

|}

Bioinfolocal:storagenet

Gianluca — Thu, 14 Feb 2008 11:29:41 GMT

Summary: [[Bioinfolocal:storagenet]] moved to [[biolocal:Storagenet]]: moving to the right namespace

[[Image:SANarchitecture.jpg]]

== Storage description ==
The central storage is composed of 20 FC disks of 300Gb 10000RPM and 70 SATA II disks of 750Gb 7200RPM.
It is managed by using a double cotroller with 2+2 FC ports, connected to the SAN switch in a redundancy and fail over configuration.
Each controller also allows to connect 4 iSCSI hosts.

== Host connectivity ==
There are 2 hosts connected to the SAN by using 2 FC adapters for redundancy and failover capabilities and 6 hosts with a single FC connection to the SAN switch.

Four of the eight iSCSI ports on the storage processors are also used to initialize the storage volumes on the cluster nodes; each couple of iSCSI ports coming from a single storage processor is connected to an half part of the cluster (28 nodes), featuring a dedicated access to the storage for each part of the cluster.

Have a look at the [[Hardware]] section for more information on cluster composition.

Bioinfolocal:wiki client

Gianluca — Wed, 06 Feb 2008 17:32:05 GMT

Summary: [[Bioinfolocal:wiki client]] moved to [[biolocal:Wiki client]]: moving to the right namespace

To commit wiki contents to the wikiserver use the mvs command [http://search.cpan.org/~markj/WWW-Mediawiki-Client-0.31/bin/mvs]

It is installed on the UI server ([[bioinfolocal:bioinfogroupMng|Bioinfo group server access]]).

Bioinfolocal:Write the script documentation

Luca — Mon, 04 Feb 2008 16:27:28 GMT

Summary: [[Bioinfolocal:Write the script documentation]] moved to [[biolocal:Write the script documentation]]: moving to the right namespace

The script documentation should be written according to php-documentator sintax. ([http://www.phpdoc.org see php documentator web-site].)

These are command line examples which create automatic generated documentations:

phpdoc -o HTML:frames:earthli -d [scripts directory] -t [output directory]

phpdoc -o HTML:frames:earthli -f [script file] -t [output directory]

Currently the generated documentation is stored on clr55.ceinge.unina.it and can be reached on http://clr55.ceinge.unina.it/biodevdoc/

The documentation have to be placed in the same directory of its script.

Tools documentation is at http://clr55.ceinge.unina.it/biodevdoc/.projects/tools/

Library documentation is at http://clr55.ceinge.unina.it/biodevdoc/.lib/lib_0.1/objects/

Bioinfolocal:shellFileEditing

Gianluca — Mon, 14 Jan 2008 10:33:52 GMT

Summary: [[Bioinfolocal:shellFileEditing]] moved to [[biolocal:ShellFileEditing]]: moving to the right namespace

Every command described here can be easily obtained in a high level scripting language (php). The use of bash is preferrable when you can't or won't set up an entire programming environement to launch simple commands against a list of text files.

'''Delete last line from a file/s'''

To obtain a text of a file without last line, just execute:

<pre>
cuttedfile=`sed '$d' filename`;
</pre>

Now you just need to write the new text in the same file:

<pre>
echo "$cuttedfile">filename;
</pre>

If you want to execute the same operation on a list of files contained in the same directory:

<pre>
for filename in `ls`; \
do \
cuttedfile=`sed '$d' $filename`; \
echo "$cuttedfile">$filename; \
done;
</pre>

Please, pay attention to the double quotes used to echo the $cuttedfile variable; they are needed to ensure the content of the text file is entirely kept (carrige returns, tabs and so on).

'''All you can do with sed on text files'''

Thinking of the above command as a wrapper to the sed command, it is possible to manipulate the text contained in a file in any way. Here follows a quick guide to use sed (note: the command used above is highlighted in red):

-------------------------------------------------------------------------
HANDY ONE-LINERS FOR SED (Unix stream editor) Apr. 26, 2004
compiled by Eric Pement - pemente[at]northpark[dot]edu version 5.4
Latest version of this file is usually at:
http://sed.sourceforge.net/sed1line.txt
http://www.student.northpark.edu/pemente/sed/sed1line.txt
This file is also available in Portuguese at:
http://www.lrv.ufsc.br/wmaker/sed_ptBR.html

FILE SPACING:

# double space a file
sed G

# double space a file which already has blank lines in it. Output file
# should contain no more than one blank line between lines of text.
sed '/^$/d;G'

# triple space a file
sed 'G;G'

# undo double-spacing (assumes even-numbered lines are always blank)
sed 'n;d'

# insert a blank line above every line which matches "regex"
sed '/regex/{x;p;x;}'

# insert a blank line below every line which matches "regex"
sed '/regex/G'

# insert a blank line above and below every line which matches "regex"
sed '/regex/{x;p;x;G;}'

NUMBERING:

# number each line of a file (simple left alignment). Using a tab (see
# note on '\t' at end of file) instead of space will preserve margins.
sed = filename | sed 'N;s/\n/\t/'

# number each line of a file (number on left, right-aligned)
sed = filename | sed 'N; s/^/ /; s/ *$.\{6,\}$\n/\1 /'

# number each line of file, but only print numbers if line is not blank
sed '/./=' filename | sed '/./N; s/\n/ /'

# count lines (emulates "wc -l")
sed -n '$='

TEXT CONVERSION AND SUBSTITUTION:

# IN UNIX ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
sed 's/.$//' # assumes that all lines end with CR/LF
sed 's/^M$//' # in bash/tcsh, press Ctrl-V then Ctrl-M
sed 's/\x0D$//' # gsed 3.02.80, but top script is easier

# IN UNIX ENVIRONMENT: convert Unix newlines (LF) to DOS format
sed "s/$/`echo -e \\\r`/" # command line under ksh
sed 's/$'"/`echo \\\r`/" # command line under bash
sed "s/$/`echo \\\r`/" # command line under zsh
sed 's/$/\r/' # gsed 3.02.80

# IN DOS ENVIRONMENT: convert Unix newlines (LF) to DOS format
sed "s/$//" # method 1
sed -n p # method 2

# IN DOS ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
# Can only be done with UnxUtils sed, version 4.0.7 or higher.
# Cannot be done with other DOS versions of sed. Use "tr" instead.
sed "s/\r//" infile >outfile # UnxUtils sed v4.0.7 or higher
tr -d \r <infile >outfile # GNU tr version 1.22 or higher

# delete leading whitespace (spaces, tabs) from front of each line
# aligns all text flush left
sed 's/^[ \t]*//' # see note on '\t' at end of file

# delete trailing whitespace (spaces, tabs) from end of each line
sed 's/[ \t]*$//' # see note on '\t' at end of file

# delete BOTH leading and trailing whitespace from each line
sed 's/^[ \t]*//;s/[ \t]*$//'

# insert 5 blank spaces at beginning of each line (make page offset)
sed 's/^/ /'

# align all text flush right on a 79-column width
sed -e :a -e 's/^.\{1,78\}$/ &/;ta' # set at 78 plus 1 space

# center all text in the middle of 79-column width. In method 1,
# spaces at the beginning of the line are significant, and trailing
# spaces are appended at the end of the line. In method 2, spaces at
# the beginning of the line are discarded in centering the line, and
# no trailing spaces appear at the end of lines.
sed -e :a -e 's/^.\{1,77\}$/ & /;ta' # method 1
sed -e :a -e 's/^.\{1,77\}$/ &/;ta' -e 's/$ *$\1/\1/' # method 2

# substitute (find and replace) "foo" with "bar" on each line
sed 's/foo/bar/' # replaces only 1st instance in a line
sed 's/foo/bar/4' # replaces only 4th instance in a line
sed 's/foo/bar/g' # replaces ALL instances in a line
sed 's/$.*$foo$.*foo$/\1bar\2/' # replace the next-to-last case
sed 's/$.*$foo/\1bar/' # replace only the last case

# substitute "foo" with "bar" ONLY for lines which contain "baz"
sed '/baz/s/foo/bar/g'

# substitute "foo" with "bar" EXCEPT for lines which contain "baz"
sed '/baz/!s/foo/bar/g'

# change "scarlet" or "ruby" or "puce" to "red"
sed 's/scarlet/red/g;s/ruby/red/g;s/puce/red/g' # most seds
gsed 's/scarlet\|ruby\|puce/red/g' # GNU sed only

# reverse order of lines (emulates "tac")
# bug/feature in HHsed v1.5 causes blank lines to be deleted
sed '1!G;h;$!d' # method 1
sed -n '1!G;h;$p' # method 2

# reverse each character on the line (emulates "rev")
sed '/\n/!G;s/$.$$.*\n$/&\2\1/;//D;s/.//'

# join pairs of lines side-by-side (like "paste")
sed '$!N;s/\n/ /'

# if a line ends with a backslash, append the next line to it
sed -e :a -e '/\\$/N; s/\\\n//; ta'

# if a line begins with an equal sign, append it to the previous line
# and replace the "=" with a single space
sed -e :a -e '$!N;s/\n=/ /;ta' -e 'P;D'

# add commas to numeric strings, changing "1234567" to "1,234,567"
gsed ':a;s/\B[0-9]\{3\}\>/,&/;ta' # GNU sed
sed -e :a -e 's/$.*[0-9]$$[0-9]\{3\}$/\1,\2/;ta' # other seds

# add commas to numbers with decimal points and minus signs (GNU sed)
gsed ':a;s/$^\|[^0-9.]$$[0-9]\+$$[0-9]\{3\}$/\1\2,\3/g;ta'

# add a blank line every 5 lines (after lines 5, 10, 15, 20, etc.)
gsed '0~5G' # GNU sed only
sed 'n;n;n;n;G;' # other seds

SELECTIVE PRINTING OF CERTAIN LINES:

# print first 10 lines of file (emulates behavior of "head")
sed 10q

# print first line of file (emulates "head -1")
sed q

# print the last 10 lines of a file (emulates "tail")
sed -e :a -e '$q;N;11,$D;ba'

# print the last 2 lines of a file (emulates "tail -2")
sed '$!N;$!D'

# print the last line of a file (emulates "tail -1")
sed '$!d' # method 1
sed -n '$p' # method 2

# print only lines which match regular expression (emulates "grep")
sed -n '/regexp/p' # method 1
sed '/regexp/!d' # method 2

# print only lines which do NOT match regexp (emulates "grep -v")
sed -n '/regexp/!p' # method 1, corresponds to above
sed '/regexp/d' # method 2, simpler syntax

# print the line immediately before a regexp, but not the line
# containing the regexp
sed -n '/regexp/{g;1!p;};h'

# print the line immediately after a regexp, but not the line
# containing the regexp
sed -n '/regexp/{n;p;}'

# print 1 line of context before and after regexp, with line number
# indicating where the regexp occurred (similar to "grep -A1 -B1")
sed -n -e '/regexp/{=;x;1!p;g;$!N;p;D;}' -e h

# grep for AAA and BBB and CCC (in any order)
sed '/AAA/!d; /BBB/!d; /CCC/!d'

# grep for AAA and BBB and CCC (in that order)
sed '/AAA.*BBB.*CCC/!d'

# grep for AAA or BBB or CCC (emulates "egrep")
sed -e '/AAA/b' -e '/BBB/b' -e '/CCC/b' -e d # most seds
gsed '/AAA\|BBB\|CCC/!d' # GNU sed only

# print paragraph if it contains AAA (blank lines separate paragraphs)
# HHsed v1.5 must insert a 'G;' after 'x;' in the next 3 scripts below
sed -e '/./{H;$!d;}' -e 'x;/AAA/!d;'

# print paragraph if it contains AAA and BBB and CCC (in any order)
sed -e '/./{H;$!d;}' -e 'x;/AAA/!d;/BBB/!d;/CCC/!d'

# print paragraph if it contains AAA or BBB or CCC
sed -e '/./{H;$!d;}' -e 'x;/AAA/b' -e '/BBB/b' -e '/CCC/b' -e d
gsed '/./{H;$!d;};x;/AAA\|BBB\|CCC/b;d' # GNU sed only

# print only lines of 65 characters or longer
sed -n '/^.\{65\}/p'

# print only lines of less than 65 characters
sed -n '/^.\{65\}/!p' # method 1, corresponds to above
sed '/^.\{65\}/d' # method 2, simpler syntax

# print section of file from regular expression to end of file
sed -n '/regexp/,$p'

# print section of file based on line numbers (lines 8-12, inclusive)
sed -n '8,12p' # method 1
sed '8,12!d' # method 2

# print line number 52
sed -n '52p' # method 1
sed '52!d' # method 2
sed '52q;d' # method 3, efficient on large files

# beginning at line 3, print every 7th line
gsed -n '3~7p' # GNU sed only
sed -n '3,${p;n;n;n;n;n;n;}' # other seds

# print section of file between two regular expressions (inclusive)
sed -n '/Iowa/,/Montana/p' # case sensitive

SELECTIVE DELETION OF CERTAIN LINES:

# print all of file EXCEPT section between 2 regular expressions
sed '/Iowa/,/Montana/d'

# delete duplicate, consecutive lines from a file (emulates "uniq").
# First line in a set of duplicate lines is kept, rest are deleted.
sed '$!N; /^$.*$\n\1$/!P; D'

# delete duplicate, nonconsecutive lines from a file. Beware not to
# overflow the buffer size of the hold space, or else use GNU sed.
sed -n 'G; s/\n/&&/; /^$[ -~]*\n$.*\n\1/d; s/\n//; h; P'

# delete all lines except duplicate lines (emulates "uniq -d").
sed '$!N; s/^$.*$\n\1$/\1/; t; D'

# delete the first 10 lines of a file
sed '1,10d'


# delete the last line of a file
sed '$d'


# delete the last 2 lines of a file
sed 'N;$!P;$!D;$d'

# delete the last 10 lines of a file
sed -e :a -e '$d;N;2,10ba' -e 'P;D' # method 1
sed -n -e :a -e '1,10!{P;N;D;};N;ba' # method 2

# delete every 8th line
gsed '0~8d' # GNU sed only
sed 'n;n;n;n;n;n;n;d;' # other seds

# delete ALL blank lines from a file (same as "grep '.' ")
sed '/^$/d' # method 1
sed '/./!d' # method 2

# delete all CONSECUTIVE blank lines from file except the first; also
# deletes all blank lines from top and end of file (emulates "cat -s")
sed '/./,/^$/!d' # method 1, allows 0 blanks at top, 1 at EOF
sed '/^$/N;/\n$/D' # method 2, allows 1 blank at top, 0 at EOF

# delete all CONSECUTIVE blank lines from file except the first 2:
sed '/^$/N;/\n$/N;//D'

# delete all leading blank lines at top of file
sed '/./,$!d'

# delete all trailing blank lines at end of file
sed -e :a -e '/^\n*$/{$d;N;ba' -e '}' # works on all seds
sed -e :a -e '/^\n*$/N;/\n$/ba' # ditto, except for gsed 3.02*

# delete the last line of each paragraph
sed -n '/^$/{p;h;};/./{x;/./p;}'

SPECIAL APPLICATIONS:

# remove nroff overstrikes (char, backspace) from man pages. The 'echo'
# command may need an -e switch if you use Unix System V or bash shell.
sed "s/.`echo \\\b`//g" # double quotes required for Unix environment
sed 's/.^H//g' # in bash/tcsh, press Ctrl-V and then Ctrl-H
sed 's/.\x08//g' # hex expression for sed v1.5

# get Usenet/e-mail message header
sed '/^$/q' # deletes everything after first blank line

# get Usenet/e-mail message body
sed '1,/^$/d' # deletes everything up to first blank line

# get Subject header, but remove initial "Subject: " portion
sed '/^Subject: */!d; s///;q'

# get return address header
sed '/^Reply-To:/q; /^From:/h; /./d;g;q'

# parse out the address proper. Pulls out the e-mail address by itself
# from the 1-line return address header (see preceding script)
sed 's/ *(.*)//; s/>.*//; s/.*[:<] *//'

# add a leading angle bracket and space to each line (quote a message)
sed 's/^/> /'

# delete leading angle bracket & space from each line (unquote a message)
sed 's/^> //'

# remove most HTML tags (accommodates multiple-line tags)
sed -e :a -e 's/<[^>]*>//g;/</N;//ba'

# extract multi-part uuencoded binaries, removing extraneous header
# info, so that only the uuencoded portion remains. Files passed to
# sed must be passed in the proper order. Version 1 can be entered
# from the command line; version 2 can be made into an executable
# Unix shell script. (Modified from a script by Rahul Dhesi.)
sed '/^end/,/^begin/d' file1 file2 ... fileX | uudecode # vers. 1
sed '/^end/,/^begin/d' "$@" | uudecode # vers. 2

# zip up each .TXT file individually, deleting the source file and
# setting the name of each .ZIP file to the basename of the .TXT file
# (under DOS: the "dir /b" switch returns bare filenames in all caps).
echo @echo off >zipup.bat
dir /b *.txt | sed "s/^$.*$\.TXT/pkzip -mo \1 \1.TXT/" >>zipup.bat

TYPICAL USE: Sed takes one or more editing commands and applies all of
them, in sequence, to each line of input. After all the commands have
been applied to the first input line, that line is output and a second
input line is taken for processing, and the cycle repeats. The
preceding examples assume that input comes from the standard input
device (i.e, the console, normally this will be piped input). One or
more filenames can be appended to the command line if the input does
not come from stdin. Output is sent to stdout (the screen). Thus:

cat filename | sed '10q' # uses piped input
sed '10q' filename # same effect, avoids a useless "cat"
sed '10q' filename > newfile # redirects output to disk

For additional syntax instructions, including the way to apply editing
commands from a disk file instead of the command line, consult "sed &
awk, 2nd Edition," by Dale Dougherty and Arnold Robbins (O'Reilly,
1997; http://www.ora.com), "UNIX Text Processing," by Dale Dougherty
and Tim O'Reilly (Hayden Books, 1987) or the tutorials by Mike Arst
distributed in U-SEDIT2.ZIP (many sites). To fully exploit the power
of sed, one must understand "regular expressions." For this, see
"Mastering Regular Expressions" by Jeffrey Friedl (O'Reilly, 1997).
The manual ("man") pages on Unix systems may be helpful (try "man
sed", "man regexp", or the subsection on regular expressions in "man
ed"), but man pages are notoriously difficult. They are not written to
teach sed use or regexps to first-time users, but as a reference text
for those already acquainted with these tools.

QUOTING SYNTAX: The preceding examples use single quotes ('...')
instead of double quotes ("...") to enclose editing commands, since
sed is typically used on a Unix platform. Single quotes prevent the
Unix shell from intrepreting the dollar sign ($) and backquotes
(`...`), which are expanded by the shell if they are enclosed in
double quotes. Users of the "csh" shell and derivatives will also need
to quote the exclamation mark (!) with the backslash (i.e., \!) to
properly run the examples listed above, even within single quotes.
Versions of sed written for DOS invariably require double quotes
("...") instead of single quotes to enclose editing commands.

USE OF '\t' IN SED SCRIPTS: For clarity in documentation, we have used
the expression '\t' to indicate a tab character (0x09) in the scripts.
However, most versions of sed do not recognize the '\t' abbreviation,
so when typing these scripts from the command line, you should press
the TAB key instead. '\t' is supported as a regular expression
metacharacter in awk, perl, and HHsed, sedmod, and GNU sed v3.02.80.

VERSIONS OF SED: Versions of sed do differ, and some slight syntax
variation is to be expected. In particular, most do not support the
use of labels (:name) or branch instructions (b,t) within editing
commands, except at the end of those commands. We have used the syntax
which will be portable to most users of sed, even though the popular
GNU versions of sed allow a more succinct syntax. When the reader sees
a fairly long command such as this:

sed -e '/AAA/b' -e '/BBB/b' -e '/CCC/b' -e d

it is heartening to know that GNU sed will let you reduce it to:

sed '/AAA/b;/BBB/b;/CCC/b;d' # or even
sed '/AAA\|BBB\|CCC/b;d'

In addition, remember that while many versions of sed accept a command
like "/one/ s/RE1/RE2/", some do NOT allow "/one/! s/RE1/RE2/", which
contains space before the 's'. Omit the space when typing the command.

OPTIMIZING FOR SPEED: If execution speed needs to be increased (due to
large input files or slow processors or hard disks), substitution will
be executed more quickly if the "find" expression is specified before
giving the "s/.../.../" instruction. Thus:

sed 's/foo/bar/g' filename # standard replace command
sed '/foo/ s/foo/bar/g' filename # executes more quickly
sed '/foo/ s//bar/g' filename # shorthand sed syntax

On line selection or deletion in which you only need to output lines
from the first part of the file, a "quit" command (q) in the script
will drastically reduce processing time for large files. Thus:

sed -n '45,50p' filename # print line nos. 45-50 of a file
sed -n '51q;45,50p' filename # same, but executes much faster

If you have any additional scripts to contribute or if you find errors
in this document, please send e-mail to the compiler. Indicate the
version of sed you used, the operating system it was compiled for, and
the nature of the problem. Various scripts in this file were written
or contributed by:

Al Aab <af137@freenet.toronto.on.ca> # "seders" list moderator
Edgar Allen <era@sky.net> # various
Yiorgos Adamopoulos <adamo@softlab.ece.ntua.gr>
Dale Dougherty <dale@songline.com> # author of "sed & awk"
Carlos Duarte <cdua@algos.inesc.pt> # author of "do it with sed"
Eric Pement <pemente@northpark.edu> # author of this document
Ken Pizzini <ken@halcyon.com> # author of GNU sed v3.02
S.G. Ravenhall <stew.ravenhall@totalise.co.uk> # great de-html script
Greg Ubben <gsu@romulus.ncsc.mil> # many contributions & much help
-------------------------------------------------------------------------

Bioinfolocal:BiodevFolder

Luca — Fri, 11 Jan 2008 17:07:55 GMT

Summary: [[Bioinfolocal:BiodevFolder]] moved to [[biolocal:BiodevFolder]]: moving to the right namespace

This folder contains all the projects implemented from [[The_bioinformatics_group|the bioinformatic group]] at Ceinge.

It is currently located on the user interface (ui.ceinge.unina.it). (see also the [[bioinfolocal:ClusterMounts|cluster mount points]])

Structure of biodev folder.

<pre>
/biodev
SLSS - > link to ./.projects/SLSS/cli_release
nonomu - > link to ./.projects/nonomu/cli_release
CSTS - > link to ./.projects/CSTS/cli_release
.....
.lib
.web/
SLSS - > link to ./.projects/SLSS/web_release
nonomu - > link to ./.projects/nonomu/web_release
CSTS - > link to ./.projects/CSTS/web_release
.projects/
nonomu/
CSTS/
...../
SLSS/
literature/
slss_article.pdf
web_release - > link to ./SLSS_0.2/web/
cli_release - > link to ./SLSS_0.2/cli/
SLSS_0.1/
SLSS_0.2/
doc/
README.txt
changelog.txt
web/
analize_SLSS.php
cli/
launch_SLSS.php
</pre>

Bioinfolocal:Start new project

Luca — Fri, 11 Jan 2008 17:04:23 GMT

Summary:

All the projects are collected in the biodev folder on the UI server.

To start a new project, please, choose a short name and submit a request to the system administrator, indicating a list of users that are allowed to manage it.

To get more information about the structure of a project and how to create it, have a look at the following links:

*[[bioinfolocal:BiodevProjectInit|project initialization]].
*[[bioinfolocal:BiodevFolder|biodev]] folder.
*[[bioinfolocal:bioinfogroupMng|Bioinfo group server access (UI server)]]

BiodevFolder

Luca — Fri, 11 Jan 2008 16:58:47 GMT

Summary: Removing all content from page

Bioinfolocal:StartNewPrj

Luca — Fri, 11 Jan 2008 16:01:19 GMT

Summary: [[Bioinfolocal:StartNewPrj]] moved to [[biolocal:StartNewPrj]]: moving to the right namespace

New projects have to be developed within biodev folder

Bioinfolocal:ClusterMounts

Luca — Fri, 11 Jan 2008 15:35:23 GMT

Summary: [[Bioinfolocal:ClusterMounts]] moved to [[biolocal:ClusterMounts]]: moving to the right namespace

[[Image:ClusterMounts.jpg]]

Bioinfolocal:gridUse

Gianluca — Tue, 13 Nov 2007 16:35:49 GMT

Summary: [[Bioinfolocal:gridUse]] moved to [[biolocal:GridUse]]: moving to the right namespace

'''Setup the access to the grid'''

The bioinfoaccess server can be used to access the SCOPE grid, by using the personal certificate, properly installed and initialized.
If you have your personal certificate already installed in your browser, export it as file and save it in your home directory, under the .globus directory.

[[Image:Cert_download.jpg]]

In the image, a certificate file will be generated and should be uploaded on the bioinfoaccess server:

<pre>
scp myCertificate.p12 gianluca@bioinfoaccess.ceinge.unina.it:
</pre>

On the bioinfo access server, some commands should still be used to have the personal certificate installed correctly:

<pre>
mkdir .globus
cd .globus
openssl pkcs12 -nocerts -in ../myCertificate.p12 -out userkey.pem
openssl pkcs12 -clcerts -nokeys -in ../myCertificate.p12 -out usercert.pem
chmod 400 userkey.pem
chmod 600 usercert.pem
</pre>

The two openssl command are needed to extract the private and public key from the pk12 certificate file. Don't forget to change the access mode of the files!

The account is now configured to provide the correct credentials when the access to the grid is requested.

'''Access and use the grid'''

Before start submitting jobs to the grid, a new proxy certificate should be created in the scope VO:

<pre>
voms-proxy-init -voms scope
</pre>

To get information about the proxy certificate, use the voms-proxy-info command. Particularly useful to know the remaining time of validity.

To execute a job a jdl file should be compiled as follows:
<pre>
Executable = "/bin/echo";
Arguments = "Hello World";
StdOutput = "message.txt";
StdError = "stderror";
OutputSandbox = {"message.txt","stderror"};
</pre>
To submit and view the state of the job use the command:
<pre>
edg-job-submit test1.jdl
edg-job-status https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
</pre>

In the above example, after the submission a url is returned to refer to the submitted job. It is used to get the status.

When the state becomes "done", the result can be retreived with the command:
<pre>
edg-job-get-output https://scoperb01.dsf.unina.it:9000/DXWtFSVPAjfLeAIBlRcfdw
</pre>

[http://mediawiki.ceinge.unina.it/files/JDL-Attributes-v0-8.pdf JDL Manual]

Bioinfolocal:bioinfogroupMng

Gianluca — Tue, 13 Nov 2007 14:34:38 GMT

Summary:

{| border="1" cellspacing="0" cellpadding="5" align="right"
!
! Uid
! Gid
|-
| giovanni
| 550
| 550
|-
|-
| gianluca
| 551
| 551
|-
|-
| mauro
| 552
| 552
|-
|-
| angelo
| 553
| 553
|-
|-
| vittorio
| 554
| 554
|-
|-
| luca
| 555
| 555
|-
|-
| concita
| 556
| 556
|-
|-
| leandra
| 557
| 557
|-
|-
| angela
| 558
| 558
|-
|-
| marisa
| 559
| 559
|-
|-
| paolo
| 560
| 560
|-
|-
| pippi
| 561
| 561
|-
|-
| nunzia
| 564
| 564
|-
|}

'''UIDs and GIDs assignement'''

Each username is associated with a numeric id to manage the ownership of the files. The user lists on the servers are configured following a predefined schema, as shown in the table.

'''Server access'''

Each registered user can access by ssh the server:

bioinfoaccess.ceinge.unina.it

This server is accessible from any internet address and can be used to reach servers closed to the external network.

'''Access to the cluster network'''

The bioinfoAccess.ceinge.unina.it server can also be used to access to the cluster network, by using a dedicated interface configured on the 192.168.151.x network; the IP interface is:

192.168.151.184

'''Working on the cluster network'''

Coming soon...

Bioinfolocal:FShomesRecover

Gianluca — Tue, 09 Oct 2007 16:53:55 GMT

Summary:

The following procedure provides a way to recover the homes of the ceinge file server whenever a disk failure occurs. It is based on maildir folder syncronization with the backup server. This way, it is possible to switch the mailserver on before the entire sync is completed.
Before any rebuild from the backup data, please make sure every attempt to recover the disks is made; particularly, in case of linux raid disks [[biolocal:linux raid|try this]].

Connect to the File Server 143.225.151.27

Recover the disk and make the base directory for the ceinge homes:

<pre>
mkdir /data01/FS /data01/FS/ceinge /data01/FS/ceinge/Home
</pre>

Connect to the backup server 143.225.151.42

Make the home dirs without descending into them (-pogdv options)
<pre>
rsync -pogdv -e ssh /media/usbdisk1/FSceinge/ceinge/Home/ root@143.225.151.27:/data01/FS/ceinge/Home/
</pre>

Start syncronizing the login folder (contains Maildir)

<pre>
for i in `ls`; \
do \
echo $i; \
rsync -avz -e ssh --exclude=*archive* $i/login/ root@143.225.151.27:/data01/FS/ceinge/Home/$i/login/; \
done;
</pre>

Start the mail server:
<pre>
/etc/init.d/Mailscanner start
</pre>

Recover the archive boxes:
<pre>
for i in `ls`; \
do \
echo $i; \
rsync -avz -e ssh $i/login/Maildir/archive/ root@143.225.151.27:/data01/FS/ceinge/Home/$i/login/Maildir/archive/; \
done;
</pre>

Then syncronize the archive

Syncronize the whole home directories without the login directory (already done in the previous step)
<pre>
for i in `ls`; \
do \
rsync -avz -e ssh --exclude=login* $i/ root@143.225.151.27:/data01/FS/ceinge/Home/$i/; \
done;
</pre>

Bioinfolocal:biotmp policy

Gianluca — Fri, 05 Oct 2007 11:29:55 GMT

Summary: [[Bioinfolocal:biotmp policy]] moved to [[biolocal:Biotmp policy]]: moving to the right namespace

The configuration provides at the moment a service to remove old temporary files in /mnt/sharedtmp (mounted on the cluster as /biotmp) only for the pise program (/mnt/sharedtmp/Pise_c), excluding some functional directories (-x option):

<pre>
# remove Pise temporary files
/usr/sbin/tmpwatch --ctime \
-x /mnt/sharedtmp/Pise_c/caprilog \
-x /mnt/sharedtmp/Pise_c/alexPise \
-x /mnt/sharedtmp/Pise_c/drawplasmid \
-x /mnt/sharedtmp/Pise_c/openFile \
-x /mnt/sharedtmp/Pise_c/openFileCol \
-x /mnt/sharedtmp/Pise_c/REQUESTS \
-x /mnt/sharedtmp/Pise_c/seq \
-x /mnt/sharedtmp/Pise_c/seqDNA \
-x /mnt/sharedtmp/Pise_c/seqPRO \
-x /mnt/sharedtmp/Pise_c/SplitSeq 120 /mnt/sharedtmp/Pise_c
</pre>

Bioinfolocal:bigsis agent install

Gianluca — Thu, 04 Oct 2007 12:37:54 GMT

Summary: [[Bioinfolocal:bigsis agent install]] moved to [[biolocal:Bigsis agent install]]: moving to the right namespace

Create a group and a user with gid and id 604 named bigsis:

* groupadd -g 604 bigsis
* useradd -u 604 -g 604 bigsis

Install the agent and the libraries:

* rpm -ivh bigsister-1.02-4.noarch.rpm bigsister-agent-1.02-4.noarch.rpm
* yum install perl-GD

Configure the automatic startup:

* chkconfig --add bigsister

Modify the group and the group permissions, to allow the bigsis user to read the sistem logs:

* chown root.bigsis /var/log/messages*
* chown root.bigsis /var/log/maillog*
* chmod g+r /var/log/messages*
* chmod g+r /var/log/maillog*

Edit the /etc/logrotate.d/syslog file to ensure that the rotate log files will be created with the right permissions.

Modify the default configuration:
<pre>
/var/log/messages /var/log/secure /var/log/maillog /var/log/spooler /var/log/boot.log /var/log/cron {
sharedscripts
postrotate
/bin/kill -HUP `cat /var/run/syslogd.pid 2> /dev/null` 2> /dev/null || true
endscript
}
</pre>

with the following:
<pre>
/var/log/messages /var/log/maillog {
sharedscripts
create 640 root bigsis
postrotate
/bin/kill -HUP `cat /var/run/syslogd.pid 2> /dev/null` 2> /dev/null || true
endscript
}

/var/log/secure /var/log/spooler /var/log/boot.log /var/log/cron {
sharedscripts
postrotate
/bin/kill -HUP `cat /var/run/syslogd.pid 2> /dev/null` 2> /dev/null || true
endscript
}
</pre>

Configure the bigsister agent.

* cd /etc/bigsister/
* vi uxmon-net

<pre>
# KEYWORD Default settings Apply To TEST
#------------- --------------------------- -----------------
DEFAULT community=public frequency=5 perf=5 ALL
DEFAULT version=1 proto=udp rpc
DEFAULT proto=udp ping

# Information about defined systems to monitor using DESCR command.
#
# KEYWORD SYSTEM FEATURES Apply To HOST
#--------- -------------------------- ------------
DESCR features=unix,linux localhost
# DESCR features=unix,sysv,solaris someotherhost

# Run the following tests.
# Note: host1(host2) is reported under host2
# Note: host can be an IP address
# Report Host Health Test List
#------------ -----------------------------------
#localhost load memory network cpuload
#localhost disk
#localhost syslog
#localhost proc=inetd procs proc=sshd procs
#localhost users
localhost(linux1) load memory cpuload
localhost(linux1) interface=eth0 speed=1000000000 network
localhost(linux1) df="df -l" disk
localhost(linux1) syslog
localhost(linux1) proc=sshd procs
localhost(linux1) users

# EDIT THIS, replace localhost by the name or IP address of your Big Sister server
#
# BigSis Server bsdisplay /options
#------------ -----------------------------------
bpb.ceinge.unina.it bsdisplay

# include file for specific hosts, do not name it uxmon-net.* as a new
# process is started for every file matching that pattern
include include_checks.$HOST
</pre>

Start the agent.

<pre>
/etc/init.d/bigsister start
</pre>

Bioinfolocal:open firewall for proftpd

Gianluca — Thu, 04 Oct 2007 09:27:42 GMT

Summary: [[Bioinfolocal:open firewall for proftpd]] moved to [[biolocal:Open firewall for proftpd]]: moving to the right namespace

First of all restrict the data transfer in a defined range of ports, on the ftp server:

Edit the file proftpd.conf and add or modify the following line:
<pre>
PassivePorts 49152 65534 # 49152-65534, the IANA-registered ephemeral port range
</pre>

Now the iptables configuration file should be edited to allow connection on the above port range. Edit /etc/sysconfig/iptables:

<pre>
[root@bpd etc]# cat sysconfig/iptables
# Firewall configuration written by system-config-securitylevel
# Manual customization of this file is not recommended.
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
:RH-Firewall-1-INPUT - [0:0]
-A INPUT -j RH-Firewall-1-INPUT
-A FORWARD -j RH-Firewall-1-INPUT
-A RH-Firewall-1-INPUT -i lo -j ACCEPT
-A RH-Firewall-1-INPUT -p icmp --icmp-type any -j ACCEPT
-A RH-Firewall-1-INPUT -p 50 -j ACCEPT
-A RH-Firewall-1-INPUT -p 51 -j ACCEPT
-A RH-Firewall-1-INPUT -p udp --dport 5353 -d 224.0.0.251 -j ACCEPT
-A RH-Firewall-1-INPUT -p udp -m udp --dport 631 -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state ESTABLISHED,RELATED -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 10000 -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 20 -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 49152:65534 -j ACCEPT <<== Allow the tranfer on a port range
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 22 -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 21 -j ACCEPT <<== Allow the connection on port 21
-A RH-Firewall-1-INPUT -j REJECT --reject-with icmp-host-prohibited
COMMIT
</pre>

Bioinfolocal:MailServerInstall

Gianluca — Thu, 04 Oct 2007 08:45:13 GMT

Summary: [[Bioinfolocal:MailServerInstall]] moved to [[biolocal:MailServerInstall]]: moving to the right namespace

Downloads:

- mailscanner

wget http://www.mailscanner.info/files/4/rpm/MailScanner-4.61.7-2.rpm.tar.gz

- Clam+spamassassin

wget http://www.mailscanner.info/files/4/install-Clam-0.90.3-SA-3.2.1.tar.gz

- razor

wget http://surfnet.dl.sourceforge.net/sourceforge/razor/razor-agents-2.84.tar.bz2

wget http://prdownloads.sourceforge.net/razor/razor-agents-sdk-2.07.tar.bz2?download

- dcc

wget http://www.rhyolite.com/anti-spam/dcc/source/dcc.tar.Z

dcc installation:

cd dcc-1.3.57/

./configure

make

make install

Razor installation:

bunzip2 /root/mailserver/razor-agents-sdk-2.07.tar.bz2

bunzip2 /root/mailserver/razor-agents-2.84.tar.bz2

tar xvf /root/mailserver/razor-agents-sdk-2.07.tar

tar xvf /root/mailserver/razor-agents-2.84.tar

cd razor-agents-sdk-2.07/

perl Makefile.PL

make

make test

make install

cd razor-agents-2.84/

perl Makefile.PL

make

make test

make install

Clam+spamassassin installation:

tar xvzf /root/mailserver/install-Clam-0.90.3-SA-3.2.1.tar.gz

cd install-Clam-0.90.3-SA-3.2.1

./install.sh

Mailscanner installation:

./install.sh (installs all the needed perl modules)

Bioinfolocal:httpdOnCluster

Gianluca — Thu, 04 Oct 2007 08:44:04 GMT

Summary: [[Bioinfolocal:httpdOnCluster]] moved to [[biolocal:HttpdOnCluster]]: moving to the right namespace

Extract the apache package and cd into the main source directory

Edit the file containing all the the predefined profiles:

vi config.layout

Add:

<pre>
# My layout
<Layout cluster>
prefix: /opt/apache2
exec_prefix: ${prefix}
bindir: ${exec_prefix}/bin
sbindir: ${exec_prefix}/sbin
libdir: ${exec_prefix}/lib
libexecdir: ${exec_prefix}/libexec
mandir: ${prefix}/man
sysconfdir: ${prefix}/etc
datadir: ${prefix}/www
installbuilddir: ${datadir}/build
errordir: ${datadir}/error
iconsdir: ${datadir}/icons
htdocsdir: ${datadir}/htdocs
manualdir: ${datadir}/manual
cgidir: ${datadir}/cgi-bin
includedir: ${prefix}/include
localstatedir: /var
runtimedir: ${localstatedir}/run
logfiledir: ${localstatedir}/log/apache2
proxycachedir: ${localstatedir}/cache/apache2
</Layout>
</pre>

Make the compilation steps, using the cutomized configuration layout:

./configure --with-layout=cluster

make

make install

Edit the httpd.conf file and perform the following actions:

vi /opt/apache2/conf/httpd.conf

Modify:
<pre>
< User daemon
< Group daemon
---
> User apache
> Group apache
</pre>

Add:

<pre>
# PHP include
Include conf/extra/httpd-php.conf
</pre>

Add the file /opt/apache2/conf/extra/httpd-php.conf:

<pre>
#
# PHP is an HTML-embedded scripting language which attempts to make it
# easy for developers to write dynamically generated webpages.
#
LoadModule php5_module modules/libphp5.so

#
# Cause the PHP interpreter to handle files with a .php extension.
#
AddHandler php5-script .php
AddType text/html .php

#
# Add index.php to the list of files that will be served as directory
# indexes.
#
DirectoryIndex index.php

#
# Uncomment the following line to allow PHP to pretty-print .phps
# files as PHP source code:
#
#AddType application/x-httpd-php-source .phps
</pre>

Bionfolocal:MailServerInstall

Gianluca — Thu, 04 Oct 2007 08:02:16 GMT

Summary:

Bioinfolocal:ed4VpnFromCeinge

Gianluca — Mon, 06 Aug 2007 10:35:36 GMT

Summary:

[[Image:VPNdiamante.jpg]]

Personal web site

Gianluca — Fri, 29 Jun 2007 11:09:28 GMT

Summary:

[[Image:paolella_site.jpg|right]]
The CEINGE users can publish thier html documents by using the CEINGE official website www.ceinge.unina.it; to reach via web these areas, put the ~username to the end of the ceinge address:

www.ceinge.unina.it/~username

In the figure you can see how a default web page looks.

To edit and customize the default page some basic html knowledge is required; anyway an easy procedure to publish a personal web page is to write down a document with MsWord or OpenOffice Writer and save it as html file.
To publish it, save the html file on the [[User_Space_Structure|fileserver in the Sites folder]]; the starting page must be named as index.html.

<pre>
Note: The tilde character (~) is not present on the italian keyboard
and should be edited by combining a key sequence:

On Macintosh:
keep the ALT key pressed and press 5
On Windows:
keep the ALT key pressed and press the sequence 126 on the keypad
On linux:
keep the ALT key pressed and press ì
</pre>

Metabolic pathway databases

Giovanni — Wed, 27 Jun 2007 22:57:23 GMT

Summary: New page: *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PATHWAY PATHWAY]'': Kyoto Encyclopedia of Genes and Genomes (KEGG) *''[http://bioinfo.ceinge.u...

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PATHWAY PATHWAY]'': Kyoto Encyclopedia of Genes and Genomes (KEGG)
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+LENZYME LENZYME]'': Ligand Chemical Database for Enzyme Reactions
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+LCOMPOUND LCOMPOUND]'': Ligand Chemical Database for Enzyme Reactions
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+ENZYME ENZYME]'': Database of enzyme nomenclature

Outlook

Vittorio — Wed, 27 Jun 2007 07:03:20 GMT

Summary:

[[Image:logo_outlook.jpg]]
#Start Microsoft Outlook
#On the '''Tools''' menu, click '''E-mail Accounts.'''
#Click '''Add a new e-mail account''' and then click '''Next.''' [[Image:xp_01.jpg]]
#For server type, click '''POP3''' or '''IMAP''' and then click '''Next.''' [[Image:xp_02.jpg]]
#Enter the following settings: - '''Your Name:''' Name and Surname - '''E-mail Address:''' your CEINGE email address - '''User Name:''' your username - '''Password:''' leave blank - '''Remember Password:''' unchecked - '''Log on using Secure Password Authentication (SPA):''' unchecked - '''Incoming server (POP3):''' mailcheck.ceinge.unina.it - '''Outgoing mail server (SMTP):''' mailsend.ceinge.unina.it [[Image:oxp_smtp_06.jpg]]
#Click the '''More Settings''' button.
#With the '''General''' tab selected, enter a name for your mail account, such as CEINGE Email. Otherwise, the mail account name defaults to the incoming server name, which is localhost. Click '''OK.''' [[Image:oxp_004.jpg]]

Reference databases

Giovanni — Mon, 25 Jun 2007 18:27:29 GMT

Summary: New page: *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+TAXONOMY TAXONOMY]'': Contains names of all organisms represented in sequence databases by at l...

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+TAXONOMY TAXONOMY]'': Contains names of all organisms represented in sequence databases by at least one nucleotide or protein sequence
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GENETICCODE GENETICCODE]'': NCBI database of genetic codes
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+OMIM OMIM]'': Online Mendelian Inheritance in Man database.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REBASE REBASE]'': Restriction Enzyme database.

3D structures databases

Giovanni — Mon, 25 Jun 2007 18:25:38 GMT

Summary: New page: *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+NRL3D NRL3D]'': PIR-NRL3D Sequence-Structure Database. *''[http://bioinfo.ceinge.unina.it/srs71...

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+NRL3D NRL3D]'': PIR-NRL3D Sequence-Structure Database.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PDB PDB]'': Protein Data Bank (PDB) - repository for the processing and distribution of 3-D biological macromolecular structure data
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PDBFINDER PDBFINDER]'': Directory for the Brookhaven Protein Data Bank. Constructed from the PDB, DSSP and HSSP databases

Ontology databases

Giovanni — Mon, 25 Jun 2007 18:25:05 GMT

Summary: New page: *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GOA GOA]'': Gene Ontology Annotation of UniProtKb *''[http://bioinfo.ceinge.unina.it/srs7131bi...

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GOA GOA]'': Gene Ontology Annotation of UniProtKb
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+GO GO]'': GO - Geneontology Database

Protein-related databases

Giovanni — Mon, 25 Jun 2007 18:24:28 GMT

Summary: New page: *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+INTERPRO INTERPRO]'': Integrated Resource of Protein Domains and Functional Sites *''[http://bi...

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+INTERPRO INTERPRO]'': Integrated Resource of Protein Domains and Functional Sites
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IPRMATCHES IPRMATCHES]'': All hits to Swiss-Prot and TrEMBL entries in which the signatures are found by INTERPRO
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PROSITE PROSITE]'': A Dictionary of Protein Sites and Patterns - A. Bairoch
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+BLOCKS BLOCKS]'': The Blocks database of multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PRINTS PRINTS]'': Protein Motif Fingerprint Database
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMA PFAMA]'': The A division (human curated) division of the Pfam database. Alignments of protein domains and conserved regions.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMB PFAMB]'': The B division (automatically clustered) division of the Pfam database. Alignments of protein domains and conserved regions
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+SWISSPFAM SWISSPFAM]'': An annotated description of how Pfam domains map to (possibly multidomain) SwissProt entries.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMHMM PFAMHMM]'': PfamHmm database. Database of the Hidden Markov Models (HMMs) derived from the seed alignment in Pfam.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PFAMSEED PFAMSEED]'': PfamSeed database. Seed alignments (hand edited) representing each domain
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+PRODOM PRODOM]'': A comprehensive collection of protein domain families

Gene-related databases

Giovanni — Mon, 25 Jun 2007 18:23:30 GMT

Summary: New page: *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+ENTREZGENE ENTREZGENE]'': NCBI's database for gene-specific information. *''[http://bioinfo.cei...

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+ENTREZGENE ENTREZGENE]'': NCBI's database for gene-specific information.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+EPD EPD]'': Eukariotic Promoter Database - Philipp Bucher (1996)
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIGENE UNIGENE]'': Unique gene cluster db from the NCBI
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNISEQ UNISEQ]'': Sub-component of the UniGene db. Contains the sequence information from UniGene.
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UTRSITE UTRSITE]'': Sub-component of the UTRnr
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+HGBASE HGBASE]'': Human Genic Bi-Allelic Sequences Database
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHDB RHDB]'': The RHDB Radiation Hybrid Mapping Submissions database
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHEXP RHEXP]'': The RHDB Radiation Hybrid Mapping Experimental Conditions database
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHMAP RHMAP]'': The RHDB Radiation Hybrid Map Information database
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+RHPANEL RHPANEL]'': The RHPANEL RH Mapping panels database

Protein databases

Giovanni — Mon, 25 Jun 2007 18:21:48 GMT

Summary: New page: *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQP REFSEQP]'': Database of protein information from NCBI *''[http://bioinfo.ceinge.unina.i...

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQP REFSEQP]'': Database of protein information from NCBI
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIPROT UNIPROT]'': The UniProt Knowledgebase is the central database of protein sequences with accurate, consistent, *''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REMTREMBL REMTREMBL]'': REM-TrEMBL (REMaining TrEMBL) contains translations of EMBL nucleotide sequences that will not be included in TrEMBL
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIREF100 UNIREF100]'': Non redundant sequence database which combines identical sequences and sub-fragments from the same organism into a single UniRef entry
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIREF90 UNIREF90]'': A non-redundant sequence set, based on uniref100 with each sequence representing a cluster of sequence with at least 90% sequence identity
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIREF50 UNIREF50]'': A non-redundant sequence set, based on uniref100 with each sequence representing a cluster of sequences with at least 50% sequence identity
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+FANTOMp FANTOMp]'': Database of translations of mouse transcriptome
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IMGTHLA IMGTHLA]'': The IMGT/HLA Database is part of the international ImMunoGeneTics IMGT project
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IPI IPI]'': International Protein Index - a top level guide to main proteome databases
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQPNEW REFSEQPNEW]'': Database of protein information from REFSEQ RefSeq Protein Updates
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIPROT_SWISSPROT UNIPROT_SWISSPROT]'': The UniProt Knowledgebase is the central database of protein sequences with accurate, consistent, and rich sequence and functional annotation. UniProt/Swissprot contains manually-annotated records with information extracted from literature and curator-evaluated computational analysis
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UNIPROT_TREMBL UNIPROT_TREMBL]'': The UniProt Knowledgebase is the central database of protein sequences with accurate, consistent, and rich sequence and functional annotation. UniProt/Trembl consists of computationally analyzed records that await full manual annotation

DNA databases

Giovanni — Mon, 25 Jun 2007 18:19:53 GMT

Summary:

*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+EMBL EMBL]'': The EMBL nucleotide sequence database including updates
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQ REFSEQ]'': Database providing non-redundant curated data representing knowledge of known genes
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+FANTOMn FANTOMn]'': Database of mouse transcriptome
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+UTRnr UTRnr]'': 5-end and 3-end Untranslated Regions Database
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+IMGT IMGT]'': ImMunoGeneTics database. A database containing nucleotide sequences of immune system-related genes
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+EMBLWGS EMBLWGS]'': The EMBL nucleotide sequence database - whole genome shotgun sequences
*''[http://bioinfo.ceinge.unina.it/srs7131bin/cgi-bin/wgetz?_AUTHS_-AUTHE_-page+LibInfo+-lib+REFSEQNEW REFSEQNEW]'': Database providing non-redundant curated data representing knowledge of known genes RefSeq Updates

Eudora

Vittorio — Mon, 25 Jun 2007 07:28:47 GMT

Summary:

[[Image:logo_eudora.jpg]]

'''Note''': If you are upgrading from an earlier version of Eudora, your configuration settings are carried over.

The first time you launch Eudora you will be asked for some information in the Settings window. If the Settings window does not open automatically, go to the Special menu and click Settings.

#Open the Eudora Application Folder and double-click the Eudora icon. [[Image:e6_install01.jpg]]
#When asked if you want to use the system keychain, click '''No.''' [[Image:e6_install02.jpg]]
#When asked if you want to import mail from another program, click '''No''' to continue or click '''Yes''' to import settings and mail (follow the on-screen instructions). [[Image:e6_install03.jpg]]
#When asked if you want Eudora to be your default mail handler, click '''Yes''' if you want Eudora to be the mail application that opens automatically when you click on "mailto:" links on web pages. Otherwise, click '''No.''' [[Image:mail_handler.jpg]]
#Click the Getting Started icon and enter the following information: '''User Name:''' your username '''Mail Server:''' mailcheck.ceinge.unina.it '''Real Name:''' Your name as you would like it to appear in the "From:" line when you send mail. '''SMTP Server:''' mailsend.ceinge.unina.it '''Email Address:''' username@ceinge.unina.it [[Image:eudora_mac1.jpg]]
#Click the next icon in the settings window, Checking Mail: '''User Name:''' your username '''Mail Server:''' mailcheck.ceinge.unina.it '''Mail Protocol:''' POP or IMAP '''Authentication:''' Passwords '''Overlap Commands:''' unchecked '''Check for mail every __ minutes:''' If you want Eudora to automatically check for new mail, check this box and enter the frequency in minutes. ITSS recommends a setting of 15 minutes or longer. '''Leave on server for __ days:''' ITSS recommends leaving this unchecked. Leaving mail on the server leads to server overload and can cause mail quota problems if you do not perform regular maintenance. '''Delete from server when emptied from trash:''' Unchecked if you do not leave mail on the server. Checked if you leave mail on the server. [[Image:eud_mac.jpg]]
#Click the Sending Mail icon and enter the following information: '''Email Address:''' username@ceinge.unina.it '''Default Domain:''' ceinge.unina.it '''SMTP Server:''' mailsend.ceinge.unina.it '''Use submission port (587):''' unchecked '''Allow authorization:''' unchecked '''Immediate send:''' checked '''Send on check:''' checked if desired '''Use separate thread for sending:''' checked [[Image:eud_mac2.jpg]]

Bioinfo programs

Leandra — Fri, 22 Jun 2007 08:51:45 GMT

Summary:

The available tools include the full EMBOSS package, a vast collection of general purpose and more specific sequence handling programs, database search programs, such as FASTA and BLAST, CLUSTALW, programs from the PHYLIP package, a number of programs typically used for protein modelling and RNA structure analysis. Most programs are easily accessible through a Web interface, although command line access remains an option for researchers more familiar with the Unix interface. Fast and prompt execution of the programs is guaranteed by a 112 processor cluster, acting in concert with a number of smaller, multiprocessor servers; program execution is transparently uploaded to the cluster without any specific intervention from the user.

A web application developed within the group, CAPRI, allows access to the programs in a global, collective application which is run on the server, but from the point of view of the user behaves as a typical desktop application, running on each client connected to the system.

Some programs provide access to the databases. A local copy of SRS is installed and maintained; the installation is one of the most complete in terms of number of databases available and linked tools. The whole ENSEMBL genome browser, complete with all fully sequenced genomes, is also mirrored locally and made available to the users (http://ensembl.ceinge.unina.it).

All programs available may be accessed through [[PROGsDB]], a database collecting all available programs, that may be also used for access to them.

*[[EMBOSS]]
*[[PHYLIP]]
*[[HMMER]]
*[[BLAST]]
*[[SRS]]
*[[ENSEMBL]]
*[[CAPRI]]
*[[PROGsDB]]

{{footer|footername=footer biotools}}

DIAGNOSTIC

Giovanni — Fri, 22 Jun 2007 06:52:07 GMT

Summary: New page: {{footer|footername=footer facilities}}

CELLBANK

Giovanni — Fri, 22 Jun 2007 06:51:57 GMT

Summary:

The CellBank database provides a service to keep track of the propagation and storage location of samples frozen in standard cryovials and stored in the gas phase of liquid nitrogen or other commonly used freezing devices. Different kind of samples are supported such as cell lines, viruses and biological samples.
In the last years the database has been used by the CEINGE cellbank service for routine addition and removal of vials from the freezers.

A new version of the system is now completed: users can have read only access to general information about most cell lines and samples frozen by all the groups using the CellBank (but not where they are frozen), although the owner of an individual cell line can choose to keep the information hidden.
The system is also able to genereate detailed reports with the history of each vial.

Click [http://web.ceinge.unina.it/ceinge/cellbank/ here] to access the system.

{{footer|footername=footer facilities}}

OLIGOS

Giovanni — Fri, 22 Jun 2007 06:51:48 GMT

Summary:

Oligos is a database of oligonucleotides requested from the CEINGE synthesis service. The system computes and stores in a relational database various oligonucleotide properties: melting temperature, GC content, sequence length, molecular weight, scale level, purification grade. A status flag informs the user about the synthesis process.

Click [http://web.ceinge.unina.it/ceinge/oligo/ here] to access the system.

{{footer|footername=footer facilities}}

Bioinformatics

Giovanni — Thu, 21 Jun 2007 17:44:19 GMT

Summary:

=== [[Bioinfo Services|'''Bioinfo Services''']] ===
are provided through the portal at http://bioinfo.ceinge.unina.it, which gives access to a large set of services in the area of bioinformatics, which include public databases, programs and databases developed locally both as a result of specific research projects, or to solve some general experimental problems. These services are offered to the researchers at CEINGE, as well as to registered users working in other research institutions. Most services are also available to the whole scientific community.

=== '''[[Research Activity]]''' ===
is mainly centered on computational analysis of genomic sequences, mostly in the field of comparative genomics and RNA structure, but also includes functional studies of cell movement. In addition the service itself often acts as a stimulus towards the identification of new methods to solve specific problems and leads to the development of novel tools for storage and manipulation of biological data.

==='''[[IT Services]]'''===
are also provided by the people in the group, as a side activity, deriving from the need to support the development and maintenance of the data network and services such as mail, authentication, file servers etc.

[[the bioinformatics group|'''The Bioinformatics group''']] is responsible for organizing and maintaining the services and carrying out the research activity. The group, coordinated by '''[[Giovanni_Paolella|G. Paolella]]''', is composed of scientists with different backgrounds. Within it, researchers with a biological background work together with others coming from physics or informatics, to develop their research projects and provide services in the bioinformatic field.

This site is aimed to collect and present in a comfortable way services and research activity, but is also an entry point for more extensive documentation. In most cases these pages also allow direct access to the described services.

{{footer|footername=footer main}}

Giovanni Paolella

Giovanni — Thu, 21 Jun 2007 17:07:27 GMT

Summary:

{{group member|name=Giovanni|surname=Paolella|photo=giovanni_paolella|degree=Medicine|email=paolella@dbbm.unina.it|phone=+39 081 7463019}}

Storage of experimental data

Concita — Thu, 21 Jun 2007 15:50:00 GMT

Summary: New page: [[Image:ImagesDB.jpg|right|250px|images data bank]] ImagesDB was developed to store biological images together with information about the research plan, the cell line, colture conditions ...

[[Image:ImagesDB.jpg|right|250px|images data bank]]

ImagesDB was developed to store biological images together with information about the research plan, the cell line, colture conditions and the staining method and also image acquisition parameters such as objective, focus position, camera resolution, exposure time and others.
Data storage is based on a PostgreSQL relational databank. The system is organized to integrate data coming from the acquisition system, with additional experimental data directly inserted from the user. In order to facilitate storage procedures and, at the same time, to reduce errors or data loss, images and the relative data are automatically transferred into the database at the very moment they are saved.
Data access is through a user-friendly web-interface, which allows to insert, modify and search for data. Each experiment is easily connected to the corresponding research project and provides information about the samples used and their treatments. Images produced during the experiment are organized by channel, acquisition and sample. Multi level images (z-stacks or timelapse) may be individually accessed.

Image analysis and processing

Concita — Thu, 21 Jun 2007 15:38:42 GMT

Summary:

'''Image deconvolution in optical microscopy'''
[[Image:actin_original.jpg|right|150px]]

Three-dimensional optical microscopy is nowdays an efficient tool for investigation of
living biological samples. Using optical sectioning technique, a stack of 2D images is
obtained. However, due to the nature of the Optical (system) Transfer Function (OTF)
and non-optimal experimental conditions, acquired raw data are usually sensitive to some
distorsions. In order to carry out biological analysis, raw data have to be restored. The
images, obtained by a conventional fluorescence microscope, contain light from the all
3D sample-object. What is actually present in the focal plane may be blurred by “out –of -focus” fluorescence. The reduction of this effect is carried out using a unix program developed in house to execute the computational deconvolution process.
The characterisation of the out-of focus light is based on the 3D image of one point as
source, called Point Spread Function (PSF.). The PSF can be determined either
experimentally or theoretically and both methods are followed in order to have
agreement. For the experimental approach, a fluorescent microsphere is used as point
source. As best approximation, a microsphere having the diameter of about one-third
resolution size limit expected for the microscope objective used has been chosen. For the
mathematical-physical model, the PSF is assumed to have circular symmetry and is
defined by few parameters, such as the numerical aperture and magnification of each
objective, the wavelenght of the fuorescent light.
Deconvolution algorithms attempt to reassign blurred light to its location. This is
performed by reversing the convolution operation of the object with the PSF.

'''IPROC a web-system to visualize and process biological images'''
[[Image:IPROC.jpg|right|250px|IPROC]]

Digital images are in widespread use for basic research in cell and molecular biology as well as for laboratory and clinical diagnosis. Fast optical sectioning techniques, in combination with timelapse-microscopy, create big multidimensional data sets, used to image the dynamics of biological events. The management of large number of images requires the use of databases (DB), while processing of the acquired images is often necessary to enhance the visibility of cell features, that would otherwise be hidden. Several image processing options, often designed to address specific biological requirements, are available as unix programs and libraries. Their integration into a web based image processing engine, accessible online by many concurrent users, promises to be at the same time a powerful and efficient solution to deal with images in a scientific environment.
A combination of dynamic web pages, SQL database, web services and concurrent process scheduling, was used to create a system, IPROC, able to store images and have them processed interactively by a relatively large number of simultaneous users. Three independent modules cooperate to generate the interface and to insure processing, by coordinating web-page construction, image data retrieval, image processing and delivery. Processing is obtained by integrating a large library of different unix filters installed on the server, while interactivity is provided by the ability to quickly react to user input via small data requests. Filters are applied in sequence, reducing the need for temporary storage and allowing unlimited backstepping. PHP was used as the main language to build a number of objects, which together take care of obtaining images from a DB or from external files and applying the required processing steps. Wrapper objects take care of interfacing with different sets of image processing tools, available as command line programs or webservices. Adapter modules allow execution of different image processing steps in sequence.
IPROC looks like and behaves as a locally running application, while retaining the ability to take advantage of storage and computational resources available on the servers. Multidimensional images are treated as a collection of independent frames, that may be simultaneously processed. Visualization may highlight various aspects of the image data, by using a variety of display mode. The modular structure of the application permits the distribution of the various parts of the same job on different machines, thus assuring speed and low latency for operations involved in page redrawing. In a parallel environment, a large number of frames, requested by one or more users, may be calculated at the same time on different cluster nodes. Currently several processing filters have been included, by taking advantage of adapters, developed for ImageMagick and PDL libraries as well as for PHP internal image functions. Most point or area processing filters are available, as well as tools for modifying image geometry and a number of specific processing steps acting on the image as a whole, such as reslicing, projection or deconvolution. The integration of image analysis tools allows to easily produce and visualize, in text or graphic formats, histograms or other statistic measurements. A specific set of tools, independently developed for studying cell movement, is also being adapted to work within this environment.

Cell motility

Concita — Thu, 21 Jun 2007 15:19:44 GMT

Summary:

[[Image:paths.jpg|right|250px|overlay image and paths]]

A morphological and functional study of cell motility was developed by using
experimental systems able to observe cells in conditions as close as possible to
physiological ones. Cell motion was studied by video time-lapse microscopy
which allows to dinamically study cultured cells by acquiring series images
at regular time steps and by quantitatively evaluating cell movement.

'''The cell motility tool'''

In order to characterize motility, was developed software able to
draw the path followed by a cell by a list of spatial coordinates and to carry out
quantitative analysis of the paths by calculating average speed, motion coherency,
direction and other parameters.
The first results contribute to associate to different cell lines specific motion features; but a subsequent punctual analysis is included to study sub-cellular elements in order to make visible their different ability to move into the cytoplasm in response to distinct stimuli, a wound line as example. The program is wrote by PHP language, that allows the development of rather object-oriented programs and offers a high degree of easy customization. It takes in input a text file containing cartesian coordinates of each object to follow, time after time. This file is the result of a computer assisted recording of the subsequent position of the elements, stored as coordinates x and y. Starting from the ensemble of coordinates of each object to analyze, the program calculates distances and directions at each time step; then average speed, direction and tortuosity are evaluated both for each object during the whole observation period, as for the population at each time step. The list of coordinates is moreover used to draw the paths covered by the elements of the population studied. Visualization of followed paths may be superimposed on the original images and vectors, describing the observed movements, may be calculated and display in the same way. Data from the experimental observation are stored in files that may be subsequently analyzed with commonly available tools such as spreadsheet or graphic application.

'''Experimental system'''

Taking advantage of these techniques a number of
normal and transformed cell lines were studied by culturing them on plates, and
observing them under basal conditions or after stimuli. The opportunity to
dinamically and quantitatively study cell motility, allowed to highlight the effects
of single molecules. Cells transformed by overexpression of constitutively
activated variants of Ras and Src, were studied in order to determine the effect of
transformation induced by activating their respective pathways on cell motility
and to evaluate the relationship beetwen these effects and the ability of
transformed cells to form methastasis in vivo by moving to new anchorage sites.

Apple Mail

Vittorio — Thu, 21 Jun 2007 09:29:36 GMT

Summary:

# Start the OS X mail program by clicking the Mail icon in the Dock or in Applications [[Image:osx3_mail_icon.jpg]]
#Enter the following information in the Welcome to Mail window: - Account type: '''POP or IMAP''' - Account Description: Ceinge mail - Full Name: the name you want displayed on your outgoing mail - Email Address: '''username@ceinge.unina.it''' [[Image:new_account.jpg]]
#Click '''Continue'''
#Enter the following information in this window: - Incoming Mail Server: '''mailcheck.ceinge.unina.it''' - User Name: '''username''' - Password: '''leave blank''' [[Image:new_account2.jpg]]
#Next you will see an error message because you have not yet entered a password for your mail account. Click Continue [[Image:new_account3.jpg]]
#In next windows you will insert the Outgoing Mail Server (SMTP): '''mailsend.ceinge.unina.it''' end if you want to use autentication for sending email, check the box, end insert your username and password in the boxes [[Image:out.jpg]]
# In conclusion you will see the account summary [[Image:summary.jpg]]
#If you have been using another email program on your computer and would like to import the mailboxes to OS X Mail, click Yes and follow the on-screen instructions. If you do not want to import mailboxes, click done. [[Image:import.jpg]]