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April 18-22 2016
The NPS@ server will be stopped for an update of the cooling system in the computer room.

Thursday, January 14 2016
Updated broken/incorrect URL links.

Wednesday, January 13 2016
A break in services occurred from 10.00 AM to 14.00 PM. This was due to a failure in storage interface.

Thursday, December 17 2015
The storage has been changed. Services are up.

Monday, December 14-16th 2015
NPS@ will be down due to storage renewal

Monday, November 9th 2015
Fixed broken NPSA link when working with a personal sequence databank.

Monday, March 9th 2015
NPS@ is online again.

Monday, March 2nd 2015
NPS@ is offline after disk array hardware failure.

Monday, December 22nd 2014
NPS@ is online again.

Thursday, December 17th 2014
Unexpected electrical power shutdown due to a fire in a floor of the building.

Monday, December 15th 2014
Updated BLAST to version 2.2.26, to avoid error (core dump) with EMBL database.

Friday, December 12th 2014
Updated certificate to avoid error message with HTTPS.

Saturday, November 15th 2014
After a very long time UniProt Knowledge Base, Swiss-prot, Non-redundant protein, Protein Data Bank and ENA/EMBL standard sequence databanks have been updated.
Unfortunately, the updated ENA/EMBL standard sequence databank generate a core dump with blastn algorithm. We are working to fix this problem.

Tuesday, October 14th 2014
AmphipaSeek is available again.

Monday, October 6th 2014
Disulfide bridge combination number calculator is available again.

Thursday, September 18th 2014
An electrical power down of our building will require a server shutdown from 9.19 to 9.22. We apologize for any inconvenience.

Tuesday, September 2nd 2014
Hardware replacement ended. NPS@ is up and running at new URL https://npsa-prabi.ibcp.fr/.
We apologize for any inconvenience for the long downtime.
Data computed by means of NPS@ are stored for 60 days.

Monday, July 21st 2014
Hardware replacement started.

Sunday, July 13th 2014
A hardware failure causes server downtime.

Wednesday, November 14th 2013
Added calculator of disulfide bridge combination number.

Monday, August 26th 2013
Added support of the BCL2DB database sequences.

Monday, July 30th 2012
Added support of the HBVdb database.

Friday, January 20th 2012
Upload a database: fixed error message seen with blast due to FASTA header

Monday, November 28th 2011
Updated PattInProt program to solve search on non-redundant database.

Friday, August 12th 2011
Added support of the BYKdb database.

Monday, February 21st 2011
Computer replacement (SGI Altix UV and IS5000).

Tuesday, April 27th 2010
A filesystem corruption on 24th and 27th causes NPS@ service downtime.

Wednesday, August 27th 2008
Upgrade of computers that run computation of NPS@ server.
Increase speed of computation for all algorithms and especially for parallel BLAST,PSI-BLAST,FASTA,SSEARCH,ClustalW,SOPM,SOPMA.

Thursday, April 3rd 2008
NPS@ server will be stopped from Friday April 4th 2008 to Monday April 7 2008 because of power supply replacement.
Improvements:

• Computation of SOV parameter after alignment (now takes the prediction from the alignment as computed by the user) and output page (missing sequence identity line) fixed
• Multiple sequence alignment for secondary structure prediction for DSC/PHD/SOPMA built with blastp and NRPROT (instead of Swiss-Prot)

Monday, March 31st 2008
Option improvements:

• Upload database: upload of nulceotide sequence database available
• BLAST (protein) / PSI-BLAST: some options made available
• blastp: automatic adjustement of parameters for short peptide searches
• clustalw default protein pairwise alignment parameter to slow

Monday, February 11th 2008
PBIL services cluster upgraded (January 9th-January 23rd).
24 computers (6 masters + 18 computing nodes) installed (rack installation, cabling, OS installation) with 3 RAID arrays for 9 TB of disk storage
OS upgraded from RedHat ES 3 Update 6 32 bits to CentOS 5.1 64 bits

Software updated
• Apache
• Tomcat
• PERL
• Python
• Java
• PHP
• PostgreSQL
• LAM/MPI
• MPICH

Binformatics software updated/recompiled
• AMBER 9
• NAMD 2.6
• CNS 1.2
• more coming (BLAST, FastA, clustalw,...)

Problems encoutered
• 4 broken disks
• 4 RAID arrays rebuilt
• RAID drivers

Friday, September 7th 2007
10,000,000 analyses carries out by NPS@ since April 1998.

Tuesday, June 5th 2007
Broken SOPMA/SOPM/Clustal W binaries are working again

Friday, July 28th 2006

• NR protein sequence databank is now built with UniProt 70% identity and PDB sequences.
• Changed FASTA header of sequence databanks to gnl|db|seqid.

Friday, July 21th 2006
Upgraded computer cluster (42 computing CPUs).

Wednesday, June 28th 2006
New AmphipaSeek method developed in our team is available here.

Wednesday, Feburary 1st 2006
Corrected Clustal W options for nucleotide sequence alignments

Monday, January 16th 2006
Cluster of computer running NPS@ was upgraded last week (storage, cpu power).

Monday, January 2nd 2006
HAPPY NEW YEAR 2006 from the NPS@ team !
We thanks all our users for their confidence in NPS@.
During year 2005, NPS@ supports 1,687,718 analyses (7,605,760 analyses since 1998, 4,623 analyses by day).

Monday, September 26th 2005
Fixed secondary structure insertion inside multalin alignment.

Wednesday, August 17th 2005
Fixed sequence extraction problem in profile search tools: HMMSEARCH, PFSEARCH.

Tuesday, July 12th 2005
Fixed bug in secondary structure prediction consensus when individual prediction methods failed.
Improved management of secondary structure prediction in multiple sequence alignment.
Changed default methods in secondary structure prediction consensus (MLRC+PHD+DSC, better prediction quality but more CPU-time consuming).

Tuesday, May 24th 2005
NPS@ is back after a RAID disk array crash. Sorry, for any inconvenience.

Thursday, April 28th 2005
euHCVdb sequence databanks available.

• euHCVdb genome sequences contains the full-length nucleotide sequence
• euHCVdb single nucleotide sequences contains nucleotide sequence splitted by genomic regions
• euHCVdb polyprotein sequences contains translation of full-length nucleotide sequence
• euHCVdb single protein sequences contains sequences splitted by mature proteins

Wednesday, March 16th 2005
InterProScan updated with InterPro 9.0 here.

Thursday, February 3rd 2005
InterProScan updated. InterProScan v4.0 and InterPro 8.1 available here.

Monday, January 3rd 2005
HAPPY NEW YEAR 2005 from the NPS@ team.
We thanks all our users for using NPS@.
During year 2004, NPS@ supports 1,856,978 analyses (5,918,042 analyses since 1998, 5,073 analyses by day).

Monday, October 25th 2004
Note to Safari users (Apple -Mac OS X). A default timeout of 1 minute in Safari kills thes connection when the server does not send back a response during this time. There is two solutions:
- use SafariNoTimeOut (http://www.unsanity.com/haxies/snt)
- use another Web browser (Mozilla, Camino, ...)

Saturday, September 18th 2004
A problem with temporary files of PattInProt fixed.

Thursday, September 2nd 2004
5,000,000 analysis have been carried out with NPS@ (see statistics).

Tuesday, August 31st 2004
SRS to NPS@ data transfer is working again.
Secondary structure prediction in alignment is working again.

Friday, August 27th 2004
A problem in SOPMA and DSC prediction using a multiple alignment has been fixed.
Secondary structure prediction with these two methods computed between August 5th to August 26th could be wrong.

Thursday, August 5th 2004
NPS@ release 3.1 is now available !
In a constant effort to improve response time and to deal with more and more analyses, NPS@ is running on a new Linux computer cluster attached to a SAN (36 procs + 1,5 TB disk space).
Some minor bugs correted.
Tools updated when needed.
SRS updated.
Databases updates improved (Genpept no longer supported, UniProt available).
Protein secondary structure prediction in multiple sequence alignement speeded-up
Sorry for any inconvenience due to last weeks service interruption and thank you for your patience and faithfulness.
The next release of NPS@ (4.0) is scheduled in one year and will be a major release with important changes.

Monday, January 19th 2004
Last week service interruption : we are moving to a new floor in our building that means more space for the team and of course for more computers ;-).
The moving was complicated by a RAID crash and a software license problem (2 days over 3).
There will be other service interruption tomorrow and in the first weeks of February.
Sorry for any inconvenience.

Monday, January 5th 2004
HAPPY NEW YEAR 2004 from the NPS@ team.
We thanks all our users for their confidence in NPS@.
During year 2003, NPS@ supports 1,185,692 analyses (4,062,544 analyses since 1998, 3,248 analyses by day).

Tuesday, February 18th 2003
3,000,000 analysis have been carried out with NPS@ (see statistics).

Monday, February 17th 2003
In a constant effort to improve response time and to deal with more and more analyses, NPS@ is running on a Linux cluster.
There are still further improvements to do to get the best from the cluster architecture.
Some minor bugs correted.
Tools updated when needed.
SRS updated.
HMMER tool added by Céline CHARAVAY (HMMBUILD) (HMMSEARCH).
Databases updates improved.
This is NPS@ release 3.0.

Monday, January 6th 2003
NPS@ team wishes you a happy new year 2003.
Last year NPS@ carried out 2531 analyses by day (see statistics).

Monday, October 7th 2002
InterProScan to scan InterPro signatures database is available (access here).

August 2002
2,500,000 analysis have been carried out with NPS@ (see statistics).

Monday, January 28th 2002
2,000,000 analysis have been carried out with NPS@ including 400,000 Clustal W (see statistics)

Thursday, November 29th 2001

• Hardware upgrade : NPS@ is running on a more powerful server (Linux, 4-processors). We hope that you will have better response time.

Wednesday, October 17th 2001

• Superposition of 3D structures after sequence alignment is available by using the FIT program

Friday, August 24th 2001

• ESPript output added in NPS@ Clustal W output.
  ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences.

Tuesday, July 17th 2001

• New link between NPS@ and Geno3D in the NPSA link page.
• The NPS@ URL is https://npsa-prabi.ibcp.fr/.

Monday, March 5th 2001

• Geno3D : Automatic molecular modeling of proteins 3D structure is now available.
  
• AnTheProt users who want to make analyses in client/server mode must download last version of the software and set the web server to URL: http://antheprot-pbil.ibcp.fr/.
  
• MPSA users who want to make analyses in client/server must set the web server to URL: http://mpsa-pbil.ibcp.fr/.
  
• Since February 8th 2001, NPS@ new URL is https://npsa-prabi.ibcp.fr/.

Thursday, February 8th 2001

• NPS@ release 2.8 is available. New features :
  • A wait message has been added when jobs are running.
  • Sequence databanks available :
    • Bacillus subtilis protein sequences
    • GenPept (Genbank translation)
    • NPS@_3D (Sequences of known 3D structures (PDB))
    • NPS@_3D95 (Sequences of known 3D structures with 95% homology (PDB))
    • NPS@_3D25 (Sequences of known 3D structures with 25% homology (PDB))
    • NR_Prot (Non-redundant SW+SPtrEMBL+NPS@_D)
    • SWISSPROT
    • SWISSPROT+SPTrEMBL (SP-TrEMBL are sequences of TrEMBL not yet integrated in SWISSPROT)
    • TrEMBL (EMBL translation)
  • Other database : PDB and Prosite.
  • Updated version of all programs.
  • PHDhtm (for transmembrane helices prediction) added.
• SRS is now available (on SWISSPROT, SPTrEMBL and TrEMBLnew databases).
  You can directly sent sequence from SRS to NPS@ by using the LAUNCH button in SRS forms.
• The PBIL-Lyon-Gerland has opened a new service : Geno3D : Automatic modeling of proteins 3D structure.
• New ANTHEPROT URL : http://antheprot-pbil.ibcp.fr/
• New DICROPROT URL : https://dicroprot-prabi.ibcp.fr/
• New MPSA URL : http://mpsa-pbil.ibcp.fr/
• New NPS@ URL : https://npsa-prabi.ibcp.fr/
• New Geno3D service at URL : https://geno3d-prabi.ibcp.fr/
• New SRS service at URL : http://srs-pbil.ibcp.fr/

Monday, January 1st 2001
Happy new year 2001 !

Monday, August 28th 2000
1,000,000 analysis have been carried out with NPS@ including 200,000 Clustal W (see statistics)

Friday, July 28th 2000
Updated version of DSSP.
STRIDE secondary structure assignment from three-dimensional structure program added.

Tuesday, July 25th 2000
Choice between DSSP or STRIDE secondary structure data available for PREDATOR secondary structure method.

Saturday, July 15th 2000
900,000 analysis have been carried out with NPS@.

Tuesday, June 6th 2000
Bacillus subtilis protein sequence databank added.

Tuesday, May 30th 2000
Today NPS@ has been overloaded (more than 70 jobs at the same time...).
When using NPS@ web server, think that all the world can run jobs on it. So, please, wait for the server response before sending a new job (in particular if they are big). In other words, don't run simultaneously several jobs.
You can contact us for big job.
You can also contact us if you encounter some problems using NPS@ (this help us to improve it).

Wednesday, May 24th 2000
800,000 analysis have been carried out with NPS@ ( see the screenshot).

Wednesday, May 10th 2000
New BLAST and PSI-BLAST version 2.0.12 available (from NCBI).

Sunday, April 2nd 2000
700,000 analysis have been carried out with NPS@ ( see the screenshot).

Tuesday, March 14th 2000
New SOPM, SOPMA and parallel Clustal W versions
A new SOPM/SOPMA version is available.
Clustal W has been parallelized in our laboratory.

Thursday, March 9th 2000
Note for Microsoft Internet Explorer users :
In answer to many users questions, IE has an internal timeout fixed to 5 minutes. So if the computing time is above this timeout, you will not have the result.
To avoid this problem, you can :

• use Netscape Navigator
• or modify the registry as recommended by Microsoft (BE CAREFUL WHEN DOING THAT, FOR EXPERIENCED WINDOWS USER ONLY) :
  • on Microsoft support server
  • on Mike Barlotta page

Tuesday, March 7th 2000
Please, in your publication cite the NPS@ reference :
NPS@: Network Protein Sequence Analysis
TIBS 2000 March Vol. 25, No 3 [291]:147-150
Combet C., Blanchet C., Geourjon C. and Deléage G.

Moreover, we will be glad to receive a reprint of article citing NPS@.
This will be a contribution and an encouragement in developping this server.

Wednesday, February 23rd 2000
NEW ANTHEPROT release 4.7 available. New features :

• Network SOPMA secondary structure prediction
• Network PHD secondary structure prediction
• Reading of PHDsec file

Thursday, February 10th 2000
600,000 analysis have been carried out with NPS@ ( see the screenshot).

Tuesday, February the 8th 2000
The clustalw parallel version problem has been fixed. So parallel clustalw is running.

Wednesday, January the 5th 2000
Parallel version of clustalw disabled. Monoprocessor version is running. So clustalw jobs run slower.

Saturday, January 1st 2000
Happy new year 2000 !

Friday, November 26th 1999
NEW ANTHEPROT release 4.6b available.
NEW MPSA release 0.9 available (see release note).

Thursday, November 25th 1999
Databanks choice modified. Databanks available are :

• GenPept (Genbank translation)
• Non-redundant proteic sequences
• NRL_3D (Sequences of known 3D structures)
• PIR
• SWISSPROT
• SWISSPROT+SPTrEMBL (SP-TrEMBL are sequences of TrEMBL not yet integrated in SWISSPROT)
• TrEMBL (EMBL translation)

Tuesday, November 23rd 1999
500,000 analysis have been carried out with NPS@ ( see the screenshot).
The NPS@ team thanks all NPS@ users for their faith .

Wednesday, November 17th 1999
Partial extract for FASTA and SSEARCH has been corrected.

Tuesday, November 2nd 1999
CLUSTAL W 1.8 now available.

Monday, October 4th 1999
PATTINPROT search is back.

Wednesday, September 29th 1999
Sorry, PATTINPROT search temporarily disabled !

Wednesday, September 15th 1999
PROSITE database version 16 (August 1999) now available in PROSCAN.

Thursday, August 12th 1999
Because of the overloading of the server (more than 55 jobs at the same time...) and crash of it, MLRC and SOPMA secondary structure prediction methods have been removed (temporarily) from multiple alignment.
When using NPS@ web server, think that all the world can run jobs on it. So, please, wait for the server response before sending a new job (in particular if they are big). In other words, don't run simultaneously several jobs.
You can contact us for big job.
You can also contact us if you encounter some problems using NPS@ (this help us to improve it).

Monday, August 2nd 1999
The NPS@ web server release 2.5 is available at URL : https://npsa-prabi.ibcp.fr/

• On-line help available.
• New CLUSTALW interfaces. One to align nucleic acid sequences and one to align protein sequences. More secondary structure prediction methods available in the second one. For both more display options.
• New MULTALIN interfaces. One to align nucleic acid sequences and one to align protein sequences. More secondary structure prediction methods available in the second one. For both more display options.
• PHD secondary structure prediction method available.
• DSC secondary structure prediction method available.
• You can upload your own database to apply NPS@'s methods on it.
• PSI-BLAST available.
• More databases available.
• Maximum CPU time for a job is now 3 hours.

Friday, April 2nd 1999
The NPS@ web server release 2.0 is available at URL : https://npsa-prabi.ibcp.fr/

April 9th 1998
The NPS@ web server release 1.0 is available at URL : https://npsa-prabi.ibcp.fr/