https://snicdocs.nsc.liu.se/w/api.php?action=feedcontributions&user=Samuel+Lampa+%28UPPMAX%29&feedformat=atomSNIC Documentation - User contributions [en]2024-03-29T10:20:10ZUser contributionsMediaWiki 1.31.10https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=5919User:Samuel Lampa (UPPMAX)2014-09-01T21:19:21Z<p>Samuel Lampa (UPPMAX): Removed picture.</p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=50<br />
|snic ae financing=<br />
|other ae financing=BILS<br />
|financing=BILS<br />
|general activities=Graphical HPC clients and other development projects<br />
|other activities=<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
|start date=2010-10<br />
|end date=<br />
|is active=yes<br />
}}<br />
<br />
== Quick facts ==<br />
* Since Oct 2012 working 50% at UPPMAX (50% at farmbio.uu.se)<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization towards Bioinformatics).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Shell scripting]]<br />
* [[expertise::Programming]]<br />
* [[expertise::User inferface design]]<br />
* [[expertise::Go]]<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::iRODS]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]<br />
* [[expertise::Web development]]<br />
* [[expertise::Graphical design]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=5290User:Samuel Lampa (UPPMAX)2013-09-10T08:44:17Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=50<br />
|snic ae financing=<br />
|other ae financing=BILS<br />
|financing=BILS<br />
|general activities=Graphical HPC clients and other development projects<br />
|other activities=<br />
|image=Samuel.png<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
}}<br />
<br />
== Quick facts ==<br />
* Since Oct 2012 working 50% at UPPMAX (50% at farmbio.uu.se)<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization towards Bioinformatics).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Shell scripting]]<br />
* [[expertise::Programming]]<br />
* [[expertise::User inferface design]]<br />
* [[expertise::Go]]<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::iRODS]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]<br />
* [[expertise::Web development]]<br />
* [[expertise::Graphical design]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=5288User:Samuel Lampa (UPPMAX)2013-09-10T08:43:14Z<p>Samuel Lampa (UPPMAX): /* Expertise */</p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=100<br />
|snic ae financing=<br />
|other ae financing=BILS<br />
|financing=BILS (50%)<br />
|general activities=Graphical HPC clients and other development projects<br />
|other activities=<br />
|image=Samuel.png<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
}}<br />
<br />
== Quick facts ==<br />
* Since Oct 2012 working 50% at UPPMAX (50% at farmbio.uu.se)<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization towards Bioinformatics).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Shell scripting]]<br />
* [[expertise::Programming]]<br />
* [[expertise::User inferface design]]<br />
* [[expertise::Go]]<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::iRODS]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]<br />
* [[expertise::Web development]]<br />
* [[expertise::Graphical design]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=5287User:Samuel Lampa (UPPMAX)2013-09-10T08:41:50Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=100<br />
|snic ae financing=<br />
|other ae financing=BILS<br />
|financing=BILS (50%)<br />
|general activities=Graphical HPC clients and other development projects<br />
|other activities=<br />
|image=Samuel.png<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
}}<br />
<br />
== Quick facts ==<br />
* Since Oct 2012 working 50% at UPPMAX (50% at farmbio.uu.se)<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization towards Bioinformatics).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Shell scripting]]<br />
* [[expertise::Go]]<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::iRODS]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=3909User:Samuel Lampa (UPPMAX)2012-04-27T09:38:55Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=100<br />
|snic ae financing=<br />
|other ae financing=SciLifeLab, UPPMAX, and SweStore<br />
|financing=SciLifeLab (50%), UPPMAX (25%), SweStore (25%)<br />
|general activities=Automated data handling for NextGen Sequencing data, Graphical HPC clients.<br />
|other activities=<br />
|image=Samuel.png<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
}}<br />
<br />
== Quick facts ==<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization towards Bioinformatics).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::iRODS]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=3908User:Samuel Lampa (UPPMAX)2012-04-27T09:37:11Z<p>Samuel Lampa (UPPMAX): /* Quick facts */</p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=100<br />
|snic ae financing=<br />
|other ae financing=SciLifeLab, UPPMAX, and SweStore<br />
|financing=SciLifeLab (50%), UPPMAX (25%), SweStore (25%)<br />
|general activities=Development of automated data handling for NextGen Sequencing data, and graphical interfaces to HPC systems.<br />
|other activities=<br />
|image=Samuel.png<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
}}<br />
<br />
== Quick facts ==<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization towards Bioinformatics).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::iRODS]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=3907User:Samuel Lampa (UPPMAX)2012-04-27T09:35:53Z<p>Samuel Lampa (UPPMAX): /* Expertise */ Added iRODS as expertise</p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=100<br />
|snic ae financing=<br />
|other ae financing=SciLifeLab, UPPMAX, and SweStore<br />
|financing=SciLifeLab (50%), UPPMAX (25%), SweStore (25%)<br />
|general activities=Development of automated data handling for NextGen Sequencing data, and graphical interfaces to HPC systems.<br />
|other activities=<br />
|image=Samuel.png<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
}}<br />
<br />
== Quick facts ==<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization courses and degree project in Bioinformatics/Systems biology).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::iRODS]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-dCache&diff=3906Swestore-dCache2012-04-27T09:34:14Z<p>Samuel Lampa (UPPMAX): /* Unified environment */</p>
<hr />
<div>SNIC is building a storage infrastructure to complement the computational resources.<br />
<br />
Many forms of automated measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.<br />
<br />
== National storage ==<br />
<br />
The aim of the nationally accessible storage is to build a robust, flexible and expandable system that can<br />
be used in most cases where access to large scale storage is needed. To the user it should appear as a single large system,<br />
while it is desirable that some parts of the system are distributed across all SNIC centra to benefit from the advantages<br />
of, among other things, locality and cache effects. The system is intended as a versatile long-term storage system.<br />
<br />
Swestore is collaboration with this groups [http://www.ecds.se ECDS], [http://snd.gu.se SND], Biomiage, [http://www.bils.se BILS], [http://www.uppnex.uu.se UPPNEX],[http://http://lcg.web.cern.ch/lcg/public/ WLCG], [http://www.nrm.se/ NaturHistoriska RiksMuseet].<br />
<br />
Before you apply for storage to Swestore, please check if our collaborators cover your research area, and first read their information about applying for SweStore storage.<br />
<br />
* [[SweStore introduction]]<br />
* [[Apply for storage on SweStore|Apply for storage or renew apply]] <br />
* [http://status.swestore.se/munin/monitor/monitor/ Per Project Monitoring of Swestore usage]<br />
* [[Grid certificates|Getting and using certificates]]<br />
* [[Accessing SweStore national storage with the ARC client]]<br />
* [[Mounting SweStore national storage via WebDAV|Mounting SweStore national storage via WebDAV (Not recomendated at the moment)]]<br />
<br />
Support: [mailto:swestore-support@snic.vr.se swestore-support]<br />
<br />
===Example of storage project===<br />
<br />
Below are some examples of project that are using SweStore today.<br />
<br />
{|border="1" style="text-align:left; border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000" class="wikitable sortable" valign=top<br />
!Allocation name<br />
!Size in TB<br />
!class="unsortable"|Project full name<br />
|-<br />
|alice<br />
|400<br />
|<br />
|-<br />
|uppnex<br />
|140<br />
|[https://www.uppnex.uu.se UPPmax NExt Generation Sequencing Cluster & Storage]<br />
|-<br />
|brain_protein_atlas<br />
|10<br />
|Mouse brain protein atlas project<br />
|-<br />
| scims2lab<br />
|20<br />
| Identification of novel gene models by matching mass spectrometry data against 6-frame translations of the human genome<br />
|-<br />
|subatom<br />
|<br />
|Low-energy nuclear theory and experiment<br />
|-<br />
|genomics-gu<br />
|10<br />
|Genomics Core Facility, Sahlgrenska academy at University of Gothenburg.<br />
|-<br />
|Chemo<br />
|5TB<br />
|Genetic interaction networks in human deseas<br />
|-<br />
|cesm1_holocene<br />
|30<br />
|Arctic sea ice in warm climates<br />
|}<br />
<br />
== Center storage ==<br />
<br />
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre, and a unified structure and nomenclature for all centra. Unlike cluster storage which is tightly associated with a single cluster, and thus has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.<br />
<br />
=== Unified environment ===<br />
<br />
To make the usage more transparent for SNIC users, a set of environment variables are available on all SNIC resources:<br />
<br />
* <code>SNIC_BACKUP</code> – the user's primary directory at the centre<br>(the part of the centre storage that is backed up)<br />
<br />
* <code>SNIC_NOBACKUP</code> – recommended directory for project storage without backup<br>(also on the centre storage)<br />
<br />
* <code>SNIC_TMP</code> – recommended directory for best performance during a job<br>(local disk on nodes if applicable)<br />
<br />
[[Category:Storage]]<br />
[[Category:SweStore]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-dCache&diff=3905Swestore-dCache2012-04-27T09:33:50Z<p>Samuel Lampa (UPPMAX): Various adjusments</p>
<hr />
<div>SNIC is building a storage infrastructure to complement the computational resources.<br />
<br />
Many forms of automated measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.<br />
<br />
== National storage ==<br />
<br />
The aim of the nationally accessible storage is to build a robust, flexible and expandable system that can<br />
be used in most cases where access to large scale storage is needed. To the user it should appear as a single large system,<br />
while it is desirable that some parts of the system are distributed across all SNIC centra to benefit from the advantages<br />
of, among other things, locality and cache effects. The system is intended as a versatile long-term storage system.<br />
<br />
Swestore is collaboration with this groups [http://www.ecds.se ECDS], [http://snd.gu.se SND], Biomiage, [http://www.bils.se BILS], [http://www.uppnex.uu.se UPPNEX],[http://http://lcg.web.cern.ch/lcg/public/ WLCG], [http://www.nrm.se/ NaturHistoriska RiksMuseet].<br />
<br />
Before you apply for storage to Swestore, please check if our collaborators cover your research area, and first read their information about applying for SweStore storage.<br />
<br />
* [[SweStore introduction]]<br />
* [[Apply for storage on SweStore|Apply for storage or renew apply]] <br />
* [http://status.swestore.se/munin/monitor/monitor/ Per Project Monitoring of Swestore usage]<br />
* [[Grid certificates|Getting and using certificates]]<br />
* [[Accessing SweStore national storage with the ARC client]]<br />
* [[Mounting SweStore national storage via WebDAV|Mounting SweStore national storage via WebDAV (Not recomendated at the moment)]]<br />
<br />
Support: [mailto:swestore-support@snic.vr.se swestore-support]<br />
<br />
===Example of storage project===<br />
<br />
Below are some examples of project that are using SweStore today.<br />
<br />
{|border="1" style="text-align:left; border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000" class="wikitable sortable" valign=top<br />
!Allocation name<br />
!Size in TB<br />
!class="unsortable"|Project full name<br />
|-<br />
|alice<br />
|400<br />
|<br />
|-<br />
|uppnex<br />
|140<br />
|[https://www.uppnex.uu.se UPPmax NExt Generation Sequencing Cluster & Storage]<br />
|-<br />
|brain_protein_atlas<br />
|10<br />
|Mouse brain protein atlas project<br />
|-<br />
| scims2lab<br />
|20<br />
| Identification of novel gene models by matching mass spectrometry data against 6-frame translations of the human genome<br />
|-<br />
|subatom<br />
|<br />
|Low-energy nuclear theory and experiment<br />
|-<br />
|genomics-gu<br />
|10<br />
|Genomics Core Facility, Sahlgrenska academy at University of Gothenburg.<br />
|-<br />
|Chemo<br />
|5TB<br />
|Genetic interaction networks in human deseas<br />
|-<br />
|cesm1_holocene<br />
|30<br />
|Arctic sea ice in warm climates<br />
|}<br />
<br />
== Center storage ==<br />
<br />
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre, and a unified structure and nomenclature for all centra. Unlike cluster storage which is tightly associated with a single cluster, and thus has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.<br />
<br />
=== Unified environment ===<br />
<br />
To make the usage more transparent for SNIC users, a set of environment variables are available on all SNIC resources:<br />
<br />
* <code>SNIC_BACKUP</code> – the user's primary directory at the centre<br>(the part of the centre storage<br />
that is backed up)<br />
<br />
* <code>SNIC_NOBACKUP</code> – recommended directory for project storage without backup<br>(also on<br />
the centre storage)<br />
<br />
* <code>SNIC_TMP</code> – recommended directory for best performance during a job<br>(local disk on<br />
nodes if applicable)<br />
<br />
[[Category:Storage]]<br />
[[Category:SweStore]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-dCache&diff=3903Swestore-dCache2012-04-27T08:55:29Z<p>Samuel Lampa (UPPMAX): /* National storage */ Link to Swestore usage monitoring</p>
<hr />
<div>SNIC is building a storage infrastructure to complement the computational resources.<br />
<br />
Many forms of automised measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.<br />
<br />
== National storage ==<br />
<br />
The aim of the nationally accessible storage is to build a robust, flexible and expandable system that can<br />
be used in most cases where access to large scale storage is needed. To the user it should appear as a single large system,<br />
while it is desirable that some parts of the system are distributed across all SNIC centres to benefit from the advantages<br />
of, among other things, locality and cache effects. The system is intended as a versatile long-term storage system.<br />
<br />
Swestore is collaboration with this groups [http://www.ecds.se ECDS],[http://snd.gu.se SND], Biomiage,[http://www.bils.se BILS],[http://www.uppnex.uu.se UPPNEX],[http://http://lcg.web.cern.ch/lcg/public/ WLCG],[http://www.nrm.se/ NaturHistoriska RiksMuseet]<br />
<br />
Before you apple for storage to Swestore you should check if our collaborators cover your research area and read there information about apply for storage in SweStore.<br />
<br />
* [[SweStore introduction]]<br />
* [[Apply for storage on SweStore|Apply for storage or renew apply]] <br />
* [http://status.swestore.se/munin/monitor/monitor/ Per Project Monitoring of Swestore usage]<br />
* [[Grid certificates|Getting and using certificates]]<br />
* [[Accessing SweStore national storage with the ARC client]]<br />
* [[Mounting SweStore national storage via WebDAV|Mounting SweStore national storage via WebDAV (Not recomendated at the moment)]]<br />
<br />
Support: [mailto:swestore-support@snic.vr.se swestore-support]<br><br />
===Example of storage project===<br />
<br />
Here are some example that are using SweStore today.<br />
<br />
{|border="1" style="text-align:left; border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000" class="wikitable sortable" valign=top<br />
!Allocation name<br />
!Size in TB<br />
!class="unsortable"|Project full name<br />
|-<br />
|alice<br />
|400<br />
|<br />
|-<br />
|uppnex<br />
|140<br />
|[https://www.uppnex.uu.se UPPmax NExt Generation Sequencing Cluster & Storage]<br />
|-<br />
|brain_protein_atlas<br />
|10<br />
|Mouse brain protein atlas project<br />
|-<br />
| scims2lab<br />
|20<br />
| Identification of novel gene models by matching mass spectrometry data against 6-frame translations of the human genome<br />
|-<br />
|subatom<br />
|<br />
|Low-energy nuclear theory and experiment<br />
|-<br />
|genomics-gu<br />
|10<br />
|Genomics Core Facility, Sahlgrenska academy at University of Gothenburg.<br />
|-<br />
|Chemo<br />
|5TB<br />
|Genetic interaction networks in human deseas<br />
|-<br />
|cesm1_holocene<br />
|30<br />
|Arctic sea ice in warm climates<br />
|}<br />
<br />
== Center storage ==<br />
<br />
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre and a unified structure and nomenclature for all centres. Unlike cluster storage, which is tightly associated with a single cluster and, thus, has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.<br />
<br />
To make the usage more transparent for SNIC users a set of environment variables are available on all SNIC resources:<br />
<br />
SNIC_BACKUP – the user's primary directory at the centre (the part of the centre storage<br />
that is backed up)<br />
<br />
SNIC_NOBACKUP – recommended directory for project storage without backup (also on<br />
the centre storage)<br />
<br />
SNIC_TMP – recommended directory for best performance during a job (local disk on<br />
nodes if applicable)<br />
<br />
[[Category:Storage]]<br />
[[Category:SweStore]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-dCache&diff=3902Swestore-dCache2012-04-27T08:53:26Z<p>Samuel Lampa (UPPMAX): /* Example of storage project */</p>
<hr />
<div>SNIC is building a storage infrastructure to complement the computational resources.<br />
<br />
Many forms of automised measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.<br />
<br />
== National storage ==<br />
<br />
The aim of the nationally accessible storage is to build a robust, flexible and expandable system that can<br />
be used in most cases where access to large scale storage is needed. To the user it should appear as a single large system,<br />
while it is desirable that some parts of the system are distributed across all SNIC centres to benefit from the advantages<br />
of, among other things, locality and cache effects. The system is intended as a versatile long-term storage system.<br />
<br />
Swestore is collaboration with this groups [http://www.ecds.se ECDS],[http://snd.gu.se SND], Biomiage,[http://www.bils.se BILS],[http://www.uppnex.uu.se UPPNEX],[http://http://lcg.web.cern.ch/lcg/public/ WLCG],[http://www.nrm.se/ NaturHistoriska RiksMuseet]<br />
<br />
Before you apple for storage to Swestore you should check if our collaborators cover your research area and read there information about apply for storage in SweStore.<br />
<br />
* [[SweStore introduction]]<br />
* [[Apply for storage on SweStore|Apply for storage or renew apply]] <br />
* [[Grid certificates|Getting and using certificates]]<br />
* [[Accessing SweStore national storage with the ARC client]]<br />
* [[Mounting SweStore national storage via WebDAV|Mounting SweStore national storage via WebDAV (Not recomendated at the moment)]]<br />
<br />
Support: [mailto:swestore-support@snic.vr.se swestore-support]<br><br />
===Example of storage project===<br />
<br />
Here are some example that are using SweStore today.<br />
<br />
{|border="1" style="text-align:left; border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000" class="wikitable sortable" valign=top<br />
!Allocation name<br />
!Size in TB<br />
!class="unsortable"|Project full name<br />
|-<br />
|alice<br />
|400<br />
|<br />
|-<br />
|uppnex<br />
|140<br />
|[https://www.uppnex.uu.se UPPmax NExt Generation Sequencing Cluster & Storage]<br />
|-<br />
|brain_protein_atlas<br />
|10<br />
|Mouse brain protein atlas project<br />
|-<br />
| scims2lab<br />
|20<br />
| Identification of novel gene models by matching mass spectrometry data against 6-frame translations of the human genome<br />
|-<br />
|subatom<br />
|<br />
|Low-energy nuclear theory and experiment<br />
|-<br />
|genomics-gu<br />
|10<br />
|Genomics Core Facility, Sahlgrenska academy at University of Gothenburg.<br />
|-<br />
|Chemo<br />
|5TB<br />
|Genetic interaction networks in human deseas<br />
|-<br />
|cesm1_holocene<br />
|30<br />
|Arctic sea ice in warm climates<br />
|}<br />
<br />
== Center storage ==<br />
<br />
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre and a unified structure and nomenclature for all centres. Unlike cluster storage, which is tightly associated with a single cluster and, thus, has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.<br />
<br />
To make the usage more transparent for SNIC users a set of environment variables are available on all SNIC resources:<br />
<br />
SNIC_BACKUP – the user's primary directory at the centre (the part of the centre storage<br />
that is backed up)<br />
<br />
SNIC_NOBACKUP – recommended directory for project storage without backup (also on<br />
the centre storage)<br />
<br />
SNIC_TMP – recommended directory for best performance during a job (local disk on<br />
nodes if applicable)<br />
<br />
[[Category:Storage]]<br />
[[Category:SweStore]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-dCache&diff=3901Swestore-dCache2012-04-27T08:52:35Z<p>Samuel Lampa (UPPMAX): /* Example of storage project */ Added UPPNEX</p>
<hr />
<div>SNIC is building a storage infrastructure to complement the computational resources.<br />
<br />
Many forms of automised measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.<br />
<br />
== National storage ==<br />
<br />
The aim of the nationally accessible storage is to build a robust, flexible and expandable system that can<br />
be used in most cases where access to large scale storage is needed. To the user it should appear as a single large system,<br />
while it is desirable that some parts of the system are distributed across all SNIC centres to benefit from the advantages<br />
of, among other things, locality and cache effects. The system is intended as a versatile long-term storage system.<br />
<br />
Swestore is collaboration with this groups [http://www.ecds.se ECDS],[http://snd.gu.se SND], Biomiage,[http://www.bils.se BILS],[http://www.uppnex.uu.se UPPNEX],[http://http://lcg.web.cern.ch/lcg/public/ WLCG],[http://www.nrm.se/ NaturHistoriska RiksMuseet]<br />
<br />
Before you apple for storage to Swestore you should check if our collaborators cover your research area and read there information about apply for storage in SweStore.<br />
<br />
* [[SweStore introduction]]<br />
* [[Apply for storage on SweStore|Apply for storage or renew apply]] <br />
* [[Grid certificates|Getting and using certificates]]<br />
* [[Accessing SweStore national storage with the ARC client]]<br />
* [[Mounting SweStore national storage via WebDAV|Mounting SweStore national storage via WebDAV (Not recomendated at the moment)]]<br />
<br />
Support: [mailto:swestore-support@snic.vr.se swestore-support]<br><br />
===Example of storage project===<br />
<br />
Here are some example that are using SweStore today.<br />
<br />
{|border="1" style="text-align:left; border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000" class="wikitable sortable" valign=top<br />
!Allocation name<br />
!Size in TB<br />
!class="unsortable"|Project full name<br />
|-<br />
|alice<br />
|400<br />
|<br />
|-<br />
|[https://www.uppnex.uu.se UPPNEX]<br />
|140<br />
|UPPmax NExt Generation Sequencing Cluster & Storage<br />
|-<br />
|brain_protein_atlas<br />
|10<br />
|Mouse brain protein atlas project<br />
|-<br />
| scims2lab<br />
|20<br />
| Identification of novel gene models by matching mass spectrometry data against 6-frame translations of the human genome<br />
|-<br />
|subatom<br />
|<br />
|Low-energy nuclear theory and experiment<br />
|-<br />
|genomics-gu<br />
|10<br />
|Genomics Core Facility, Sahlgrenska academy at University of Gothenburg.<br />
|-<br />
|Chemo<br />
|5TB<br />
|Genetic interaction networks in human deseas<br />
|-<br />
|cesm1_holocene<br />
|30<br />
|Arctic sea ice in warm climates<br />
|}<br />
<br />
== Center storage ==<br />
<br />
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre and a unified structure and nomenclature for all centres. Unlike cluster storage, which is tightly associated with a single cluster and, thus, has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.<br />
<br />
To make the usage more transparent for SNIC users a set of environment variables are available on all SNIC resources:<br />
<br />
SNIC_BACKUP – the user's primary directory at the centre (the part of the centre storage<br />
that is backed up)<br />
<br />
SNIC_NOBACKUP – recommended directory for project storage without backup (also on<br />
the centre storage)<br />
<br />
SNIC_TMP – recommended directory for best performance during a job (local disk on<br />
nodes if applicable)<br />
<br />
[[Category:Storage]]<br />
[[Category:SweStore]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-dCache&diff=3900Swestore-dCache2012-04-27T08:50:30Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>SNIC is building a storage infrastructure to complement the computational resources.<br />
<br />
Many forms of automised measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.<br />
<br />
== National storage ==<br />
<br />
The aim of the nationally accessible storage is to build a robust, flexible and expandable system that can<br />
be used in most cases where access to large scale storage is needed. To the user it should appear as a single large system,<br />
while it is desirable that some parts of the system are distributed across all SNIC centres to benefit from the advantages<br />
of, among other things, locality and cache effects. The system is intended as a versatile long-term storage system.<br />
<br />
Swestore is collaboration with this groups [http://www.ecds.se ECDS],[http://snd.gu.se SND], Biomiage,[http://www.bils.se BILS],[http://www.uppnex.uu.se UPPNEX],[http://http://lcg.web.cern.ch/lcg/public/ WLCG],[http://www.nrm.se/ NaturHistoriska RiksMuseet]<br />
<br />
Before you apple for storage to Swestore you should check if our collaborators cover your research area and read there information about apply for storage in SweStore.<br />
<br />
* [[SweStore introduction]]<br />
* [[Apply for storage on SweStore|Apply for storage or renew apply]] <br />
* [[Grid certificates|Getting and using certificates]]<br />
* [[Accessing SweStore national storage with the ARC client]]<br />
* [[Mounting SweStore national storage via WebDAV|Mounting SweStore national storage via WebDAV (Not recomendated at the moment)]]<br />
<br />
Support: [mailto:swestore-support@snic.vr.se swestore-support]<br><br />
===Example of storage project===<br />
<br />
Here are some example that are using SweStore today.<br />
<br />
{|border="1" style="text-align:left; border-collapse: collapse; border-width: 1px; border-style: solid; border-color: #000" class="wikitable sortable" valign=top<br />
!Allocation name<br />
!Size in TB<br />
!class="unsortable"|Project full name<br />
|-<br />
|alice<br />
|400<br />
|<br />
|-<br />
|brain_protein_atlas<br />
|10<br />
|Mouse brain protein atlas project<br />
|-<br />
| scims2lab<br />
|20<br />
| Identification of novel gene models by matching mass spectrometry data against 6-frame translations of the human genome<br />
|-<br />
|subatom<br />
|<br />
|Low-energy nuclear theory and experiment<br />
|-<br />
|genomics-gu<br />
|10<br />
|Genomics Core Facility, Sahlgrenska academy at University of Gothenburg.<br />
|-<br />
|Chemo<br />
|5TB<br />
|Genetic interaction networks in human deseas<br />
|-<br />
|cesm1_holocene<br />
|30<br />
|Arctic sea ice in warm climates<br />
|}<br />
<br />
== Center storage ==<br />
<br />
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre and a unified structure and nomenclature for all centres. Unlike cluster storage, which is tightly associated with a single cluster and, thus, has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.<br />
<br />
To make the usage more transparent for SNIC users a set of environment variables are available on all SNIC resources:<br />
<br />
SNIC_BACKUP – the user's primary directory at the centre (the part of the centre storage<br />
that is backed up)<br />
<br />
SNIC_NOBACKUP – recommended directory for project storage without backup (also on<br />
the centre storage)<br />
<br />
SNIC_TMP – recommended directory for best performance during a job (local disk on<br />
nodes if applicable)<br />
<br />
[[Category:Storage]]<br />
[[Category:SweStore]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=GCTA&diff=2989GCTA2011-10-17T12:15:19Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=A tool for Genome-wide Complex Trait Analysis |license=? |fields=Bioinformatics }} [http://gump.qimr.edu.au/gcta/index.html GCTA] (Genome-..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A tool for Genome-wide Complex Trait Analysis <br />
|license=?<br />
|fields=Bioinformatics<br />
}}<br />
[http://gump.qimr.edu.au/gcta/index.html GCTA] (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits. GCTA was developed by Jian Yang, Hong Lee, Mike Goddard and Peter Visscher and is maintained in Peter Visscher's lab at the Queensland Institute of Medical Research . GCTA currently supports the following functionalities:<br />
<br />
* Estimate the genetic relationship from genome-wide SNPs;<br />
* Estimate the inbreeding coefficient from genome-wide SNPs;<br />
* Estimate the variance explained by all the autosomal SNPs;<br />
* Partition the genetic variance onto individual chromosomes;<br />
* Estimate the genetic variance associated with the X-chromosome;<br />
* Test the effect of dosage compensation on the X-chromosome;<br />
* Predict the genome-wide additive genetic effects for individual subjects and for individual SNPs;<br />
* Estimate the LD structure encompassing a list of target SNPs;<br />
* Simulate GWAS data based upon the observed genotype data.<br />
* Convert Illumina raw genotype data into PLINK PED format.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://gump.qimr.edu.au/gcta/index.html Official website]<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/21167468 Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=GATK&diff=2988GATK2011-10-17T12:13:39Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Structured software library for writing analysis tools for next-generation sequencing data. |license=free |fields=Bioinformatics }} [http:..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Structured software library for writing analysis tools for next-generation sequencing data. <br />
|license=free<br />
|fields=Bioinformatics<br />
}}<br />
[http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit GATK] is a structured software library for writing analysis tools for next-generation sequencing data. <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit Official website]<br />
* [http://genome.cshlp.org/content/early/2010/08/04/gr.107524.110.abstract Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=GARLI&diff=2987GARLI2011-10-17T12:12:36Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Performs heuristic phylogenetic searches ... |license=? |fields=Bioinformatics }} [https://www.nescent.org/wg_garli/Main_Page GARLI] perfor..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Performs heuristic phylogenetic searches ...<br />
|license=?<br />
|fields=Bioinformatics<br />
}}<br />
[https://www.nescent.org/wg_garli/Main_Page GARLI] performs heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution and its submodels, with or without gamma distributed rate heterogeneity and a proportion of invariant sites. <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [https://www.nescent.org/wg_garli/Main_Page Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=FreeBayes&diff=2986FreeBayes2011-10-17T12:11:13Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Bayesian SNP and short indel caller from the Marth lab (who created Mosaik). |license=? |fields=Bioinformatics }} [https://github.com/ekg/..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Bayesian SNP and short indel caller from the Marth lab (who created Mosaik). <br />
|license=?<br />
|fields=Bioinformatics<br />
}}<br />
[https://github.com/ekg/freebayes FreeBayes] is a bayesian SNP and short indel caller from the Marth lab (who created Mosaik). <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
Usage:<br />
module load bioinfo-tools freebayes/[version]<br />
freebayes [flags]<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [https://github.com/ekg/freebayes Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=FastQC&diff=2985FastQC2011-10-17T12:08:12Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. |lic..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. <br />
|license=free<br />
|fields=Bioinformatics<br />
}}<br />
[http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC] aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=FASTX&diff=2984FASTX2011-10-17T12:06:26Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |license=free |fields=Bioinformatics }} The [http://han..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.<br />
|license=free<br />
|fields=Bioinformatics<br />
}}<br />
The [http://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit] is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.illumina.com/software/genome_analyzer_software.ilmn Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=EMMAX&diff=2983EMMAX2011-10-17T12:03:54Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=A statistical test for large scale human or model organism association mapping accounting for the sample structure. |license=? |fields=Bio..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A statistical test for large scale human or model organism association mapping accounting for the sample structure. <br />
|license=?<br />
|fields=Bioinformatics<br />
}}<br />
[http://genetics.cs.ucla.edu/emmax/ EMMAX] is a statistical test for large scale human or model organism association mapping accounting for the sample structure. <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://genetics.cs.ucla.edu/emmax/ Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=EMBOSS&diff=2982EMBOSS2011-10-17T12:02:30Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=A free Open Source software analysis package developed for the molecular biology. |license=free |fields=Bioinformatics }} [http://www.ncbi..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A free Open Source software analysis package developed for the molecular biology. <br />
|license=free<br />
|fields=Bioinformatics<br />
}}<br />
[http://www.ncbi.nlm.nih.gov/pubmed/10827456 EMBOSS] is a free Open Source software analysis package developed for the molecular biology.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/10827456 Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Cufflinks&diff=2981Cufflinks2011-10-17T12:01:17Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Assembles transcripts in RNA-Seq samples and calculates their abundances |license=free |fields=Bioinformatics }} [http://cufflinks.cbcb.umd..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Assembles transcripts in RNA-Seq samples and calculates their abundances<br />
|license=free<br />
|fields=Bioinformatics<br />
}}<br />
[http://cufflinks.cbcb.umd.edu/ Cufflinks] is designed to assemble the transcripts in an RNA-Seq sample and calculate their abundances (in transcript-level RPKM).<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://cufflinks.cbcb.umd.edu/ Official website]<br />
* [http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Concaterpillar&diff=2980Concaterpillar2011-10-17T11:59:00Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=A hierarchical likelihood ratio test for phylogenetic congruence. |license=free |fields=Bioinformatics }} [http://rogerlab.biochemistryand..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A hierarchical likelihood ratio test for phylogenetic congruence. <br />
|license=free<br />
|fields=Bioinformatics<br />
}}<br />
[http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm#Concaterpillar Concaterpillar] is a hierarchical likelihood ratio test for phylogenetic congruence.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm#Concaterpillar Official website]<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/18288620 Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=CASAVA&diff=2979CASAVA2011-10-17T11:56:37Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software <br />
|license=?<br />
|fields=Bioinformatics<br />
}}<br />
[http://www.illumina.com/software/genome_analyzer_software.ilmn Illumina's Consensus Assessment of Sequence and Variation (CASAVA)] software captures summary information for resequencing and counting studies <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.illumina.com/software/genome_analyzer_software.ilmn Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=CASAVA&diff=2978CASAVA2011-10-17T11:55:48Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software |license=site-license |fields=Bioinformatics }} [http://www.il..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software <br />
|license=site-license<br />
|fields=Bioinformatics<br />
}}<br />
[http://www.illumina.com/software/genome_analyzer_software.ilmn Illumina's Consensus Assessment of Sequence and Variation (CASAVA)] software captures summary information for resequencing and counting studies <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.illumina.com/software/genome_analyzer_software.ilmn Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Bowtie&diff=2977Bowtie2011-10-17T11:52:55Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Bowtie is an ultrafast, memory-efficient short read aligner. |license=free |fields=Bioinformatics }} [http://bowtie-bio.sourceforge.net/in..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Bowtie is an ultrafast, memory-efficient short read aligner. <br />
|license=free<br />
|fields=Bioinformatics<br />
}}<br />
[http://bowtie-bio.sourceforge.net/index.shtml {{PAGENAME}}] is an ultrafast, memory-efficient short read aligner.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://bowtie-bio.sourceforge.net/index.shtml Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Accessing_Swestore_with_davfs2&diff=2887Accessing Swestore with davfs22011-10-04T12:15:19Z<p>Samuel Lampa (UPPMAX): /* More Hints */</p>
<hr />
<div>[[Category:SweStore]]<br />
[[Swestore national storage|< Swestore national storage]]<br />
<br />
This guide describes how to mount a folder of the SweStore National Storage as a read/writeable folder in your local file-system.<br />
<br />
== Caveat ==<br />
'''There is currently a big problem with using Davfs2 with Swestore:''' Davfs2 does not currently support Status 302 redirects, which is used by default on Swestore, to redirect you directy to the storage pools for reading (writing is done via central server though). This will cause you problems!<br />
<br />
An issue for the problem is filed here: https://savannah.nongnu.org/support/?107402<br />
<br />
== Prerequisites ==<br />
* A *nix like Operating System, such as linux (possibly MacOS might work ... and possibly Windows as well, though this is not covered in this article yet).<br />
* The davfs2 package. On ubuntu, you can install it with:<br><pre>sudo apt-get install davfs2</pre><br />
<br />
== How to ==<br />
You need to use your Terena certificate files, and convert them to the PKCS#12 format.<br />
<br />
If you have them in .pem format, you can use openssl for this.<br />
<br />
You might have them in the form of the following two files:<br />
~/.globus/usercert.pem<br />
~/.globus/userkey.pem<br />
<br />
Converted these to the PKCS#12 format with:<br />
openssl pkcs12 -export -in usercert.pem -inkey userkey.pem -out MyTerenaCert.p12<br />
<br />
'''Note:''' You will first need to unlock your cert with a password you have gave when creating it. Then you need to add a password for the pkcs12 file. Remember this latter password for the later steps!<br />
<br />
Copy the p12 cert to /etc/davfs2/certs/private, as root:<br />
sudo cp MyTerenaCert.p12 /etc/davfs2/certs/private/<br />
<br />
Edit /etc/davfs2/davfs2.conf:<br />
sudo nano /etc/davfs2/davfs2.conf<br />
<br />
At the bottom, add the line:<br />
clientcert MyTerenaCert.p12<br />
<br />
Create a folder for mounting the filesystem:<br />
sudo mkdir -p /mnt/swestore<br />
<br />
Add the following line to /etc/fstab (e.g. at the end):<br />
https://webdav.swegrid.se/snic/<your-account> /mnt/swestore davfs uid=<your-username>,gid=<your-accountname>,rw,noauto 0 0<br />
<br />
Mount, according to fstab, as root:<br />
sudo mount /mnt/swestore<br />
<br />
When asking for a username and password, just press <Enter> (two times). On the third question, you are asked for the password you gave for the pkcs12 file, which you will have to type in, each time you mount this file system.<br />
<br />
Done!<br />
<br />
Now you should be able to browse to the mount point:<br />
cd /mnt/swestore<br />
ls -l<br />
<br />
You chould be able to create files with content, and read the content:<br />
echo "Testing testing 1 2 3 ..." > testfile.txt<br />
cat testfile.txt<br />
<br />
'''Note''' however, that you are not able to open the file for updating, with editors such as ''nano''.<br />
<br />
== More Hints ==<br />
In order to automatically mount the system, you will need to download the server cert and the CA cert via Firefox, and then cat them into a single file, that you place in /etc/davfs2/certs, and then add the filename of it in /etc/davfs2/davfs2.conf like so:<br />
servercert myservercert.crt<br />
<br />
(See [http://www.linuxquestions.org/questions/linux-software-2/force-accept-certificates-when-using-mount-davfs-632056/ this link] for more info)<br />
<br />
Also, you will need to add the user name and password (that you chose when generating the p12 file above) for your client certificate, to /etc/davfs2/secrets (read the help comments about how to do).<br />
<br />
== Some Links ==<br />
* [http://linux.die.net/man/8/mount.davfs Mount Davfs2 man page]<br />
* [http://security.ncsa.illinois.edu/research/grid-howtos/usefulopenssl.html How to convert PEM to PKCS#12]<br />
* [http://sysblogd.wordpress.com/2007/09/09/ubuntu-mounting-remote-filesystem-using-davfs2-fuse/ Mounting WebDav via davfs2 (Ubuntu)]<br />
* [http://ubuntuforums.org/showthread.php?t=1034909 Install server certificates in davfs2 (Ubuntu)]<br />
* [http://www.nordugrid.org/documents/certificate_howto.html Nordugrid Certificate HowTo] - Describes the userkey.pem and usercert.pem files</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Accessing_Swestore_with_davfs2&diff=2886Accessing Swestore with davfs22011-10-04T12:14:55Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>[[Category:SweStore]]<br />
[[Swestore national storage|< Swestore national storage]]<br />
<br />
This guide describes how to mount a folder of the SweStore National Storage as a read/writeable folder in your local file-system.<br />
<br />
== Caveat ==<br />
'''There is currently a big problem with using Davfs2 with Swestore:''' Davfs2 does not currently support Status 302 redirects, which is used by default on Swestore, to redirect you directy to the storage pools for reading (writing is done via central server though). This will cause you problems!<br />
<br />
An issue for the problem is filed here: https://savannah.nongnu.org/support/?107402<br />
<br />
== Prerequisites ==<br />
* A *nix like Operating System, such as linux (possibly MacOS might work ... and possibly Windows as well, though this is not covered in this article yet).<br />
* The davfs2 package. On ubuntu, you can install it with:<br><pre>sudo apt-get install davfs2</pre><br />
<br />
== How to ==<br />
You need to use your Terena certificate files, and convert them to the PKCS#12 format.<br />
<br />
If you have them in .pem format, you can use openssl for this.<br />
<br />
You might have them in the form of the following two files:<br />
~/.globus/usercert.pem<br />
~/.globus/userkey.pem<br />
<br />
Converted these to the PKCS#12 format with:<br />
openssl pkcs12 -export -in usercert.pem -inkey userkey.pem -out MyTerenaCert.p12<br />
<br />
'''Note:''' You will first need to unlock your cert with a password you have gave when creating it. Then you need to add a password for the pkcs12 file. Remember this latter password for the later steps!<br />
<br />
Copy the p12 cert to /etc/davfs2/certs/private, as root:<br />
sudo cp MyTerenaCert.p12 /etc/davfs2/certs/private/<br />
<br />
Edit /etc/davfs2/davfs2.conf:<br />
sudo nano /etc/davfs2/davfs2.conf<br />
<br />
At the bottom, add the line:<br />
clientcert MyTerenaCert.p12<br />
<br />
Create a folder for mounting the filesystem:<br />
sudo mkdir -p /mnt/swestore<br />
<br />
Add the following line to /etc/fstab (e.g. at the end):<br />
https://webdav.swegrid.se/snic/<your-account> /mnt/swestore davfs uid=<your-username>,gid=<your-accountname>,rw,noauto 0 0<br />
<br />
Mount, according to fstab, as root:<br />
sudo mount /mnt/swestore<br />
<br />
When asking for a username and password, just press <Enter> (two times). On the third question, you are asked for the password you gave for the pkcs12 file, which you will have to type in, each time you mount this file system.<br />
<br />
Done!<br />
<br />
Now you should be able to browse to the mount point:<br />
cd /mnt/swestore<br />
ls -l<br />
<br />
You chould be able to create files with content, and read the content:<br />
echo "Testing testing 1 2 3 ..." > testfile.txt<br />
cat testfile.txt<br />
<br />
'''Note''' however, that you are not able to open the file for updating, with editors such as ''nano''.<br />
<br />
== More Hints ==<br />
In order to automatically mount the system, you will need to download the server cert and the CA cert via Firefox, and then cat them into a single file, that you place in /etc/davfs2/certs, and then add the filename of it in /etc/davfs2/davfs2.conf like so:<br />
servercert myservercert.crt<br />
<br />
Also, you will need to add the user name and password (that you chose when generating the p12 file above) for your client certificate, to /etc/davfs2/secrets (read the help comments about how to do).<br />
<br />
== Some Links ==<br />
* [http://linux.die.net/man/8/mount.davfs Mount Davfs2 man page]<br />
* [http://security.ncsa.illinois.edu/research/grid-howtos/usefulopenssl.html How to convert PEM to PKCS#12]<br />
* [http://sysblogd.wordpress.com/2007/09/09/ubuntu-mounting-remote-filesystem-using-davfs2-fuse/ Mounting WebDav via davfs2 (Ubuntu)]<br />
* [http://ubuntuforums.org/showthread.php?t=1034909 Install server certificates in davfs2 (Ubuntu)]<br />
* [http://www.nordugrid.org/documents/certificate_howto.html Nordugrid Certificate HowTo] - Describes the userkey.pem and usercert.pem files</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Accessing_Swestore_with_davfs2&diff=2880Accessing Swestore with davfs22011-09-30T15:16:30Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>[[Category:SweStore]]<br />
[[Swestore national storage|< Swestore national storage]]<br />
<br />
This guide describes how to mount a folder of the SweStore National Storage as a read/writeable folder in your local file-system.<br />
<br />
== Caveat ==<br />
'''There is currently a big problem with using Davfs2 with Swestore:''' Davfs2 does not currently support Status 302 redirects, which is used by default on Swestore, to redirect you directy to the storage pools for reading (writing is done via central server though). This will cause you problems!<br />
<br />
An issue for the problem is filed here: https://savannah.nongnu.org/support/?107402<br />
<br />
== Prerequisites ==<br />
* A *nix like Operating System, such as linux (possibly MacOS might work ... and possibly Windows as well, though this is not covered in this article yet).<br />
* The davfs2 package. On ubuntu, you can install it with:<br><pre>sudo apt-get install davfs2</pre><br />
<br />
== How to ==<br />
You need to use your Terena certificate files, and convert them to the PKCS#12 format.<br />
<br />
If you have them in .pem format, you can use openssl for this.<br />
<br />
You might have them in the form of the following two files:<br />
~/.globus/usercert.pem<br />
~/.globus/userkey.pem<br />
<br />
Converted these to the PKCS#12 format with:<br />
openssl pkcs12 -export -in usercert.pem -inkey userkey.pem -out MyTerenaCert.p12<br />
<br />
'''Note:''' You will first need to unlock your cert with a password you have gave when creating it. Then you need to add a password for the pkcs12 file. Remember this latter password for the later steps!<br />
<br />
Copy the p12 cert to /etc/davfs2/certs/private, as root:<br />
sudo cp MyTerenaCert.p12 /etc/davfs2/certs/private/<br />
<br />
Edit /etc/davfs2/davfs2.conf:<br />
sudo nano /etc/davfs2/davfs2.conf<br />
<br />
At the bottom, add the line:<br />
clientcert MyTerenaCert.p12<br />
<br />
Create a folder for mounting the filesystem:<br />
sudo mkdir -p /mnt/swestore<br />
<br />
Add the following line to /etc/fstab (e.g. at the end):<br />
https://webdav.swegrid.se/snic/<your-account> /mnt/swestore davfs uid=<your-username>,gid=<your-accountname>,rw,noauto 0 0<br />
<br />
Mount, according to fstab, as root:<br />
sudo mount /mnt/swestore<br />
<br />
When asking for a username and password, just press <Enter> (two times). On the third question, you are asked for the password you gave for the pkcs12 file, which you will have to type in, each time you mount this file system.<br />
<br />
Done!<br />
<br />
Now you should be able to browse to the mount point:<br />
cd /mnt/swestore<br />
ls -l<br />
<br />
You chould be able to create files with content, and read the content:<br />
echo "Testing testing 1 2 3 ..." > testfile.txt<br />
cat testfile.txt<br />
<br />
'''Note''' however, that you are not able to open the file for updating, with editors such as ''nano''.<br />
<br />
== Some Links ==<br />
* [http://linux.die.net/man/8/mount.davfs Mount Davfs2 man page]<br />
* [http://security.ncsa.illinois.edu/research/grid-howtos/usefulopenssl.html How to convert PEM to PKCS#12]<br />
* [http://sysblogd.wordpress.com/2007/09/09/ubuntu-mounting-remote-filesystem-using-davfs2-fuse/ Mounting WebDav via davfs2 (Ubuntu)]<br />
* [http://ubuntuforums.org/showthread.php?t=1034909 Install server certificates in davfs2 (Ubuntu)]<br />
* [http://www.nordugrid.org/documents/certificate_howto.html Nordugrid Certificate HowTo] - Describes the userkey.pem and usercert.pem files</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User_talk:Samuel_Lampa_(UPPMAX)&diff=2873User talk:Samuel Lampa (UPPMAX)2011-09-30T08:49:15Z<p>Samuel Lampa (UPPMAX): Created page with "Hi, you can leave me a message on this page! --~~~~ == Talk =="</p>
<hr />
<div>Hi, you can leave me a message on this page!<br />
--[[User:Samuel Lampa (UPPMAX)|Samuel Lampa (UPPMAX)]] 10:49, 30 September 2011 (CEST)<br />
<br />
== Talk ==</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Bioscope&diff=2872Bioscope2011-09-30T08:43:59Z<p>Samuel Lampa (UPPMAX): /* Tips and tricks */</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=the pipeline stack that comes with the solid sequence platform <br />
|license=site license<br />
|fields=bioinformatics<br />
}}<br />
SOLiD [http://solidsoftwaretools.com/ {{PAGENAME}}] Bioscope provides a command line for running application-specific sequence analysis tools. The Bioscope framework enables the user to perform off-instrument secondary and tertiary analyses, and it allows configurable bioinformatics workflows for resequencing (mapping, SNP finding (diBayes), copy number variations, inversions, small indels, large indels) and whole transcriptome analysis (mapping, counting, novel transcript finding, UCSC WIG Files creation) Results will be in GFF v3 and SAM formats. The resulting industry-standard files from Bioscope can be used with third-party visualization and analysis software tools.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
On UPPMAX/[https://www.uppnex.uu.se UPPNEX] you find bioscope in the module systems on the Kalkyl cluster. <br />
<br />
Please type :<br />
module load bioinfo-tools bioscope<br />
To load the module. the command is then <br />
bioscope.sh -A b2010999<br />
To run on Kalkyl you need to specify what project shall be accounted for your job run.<br />
Bioscope integrates to the SLURM queueing system there so you only need to start bioscope.sh on a login node.<br />
We recommend you run it in the background by using "noup" <br />
nohup ./run.sh MatoBam_nohup.out<br />
Where run.sh have the run line bioscope.sh -A b2010999 -l MaToBam.log MaToBam.plan<br />
<br />
Nohup will run the job in the background and you can monitor the progress by reading the MatoBam_nohup.out.<br />
<br />
Bioscope can today use at the most 11 nodes for one bioscope run, and you can at the most start two parallel runs. This is due to the limit in the SLURM system. If you need to run several different bioscope runs. I recommend you running them one after another. <br />
<br />
Find attached the user manual to this post you need to be loged in on a registered account to read the attachment..<br />
<br />
You can also find some test data on the system under the folder:<br />
<br />
/bubo/nobackup/uppnex/bioscopedata<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://solidsoftwaretools.com/ Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Bioscope&diff=2871Bioscope2011-09-30T08:43:16Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=the pipeline stack that comes with the solid sequence platform |license=site license |fields=bioinformatics }} SOLiD [http://solidsoftware..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=the pipeline stack that comes with the solid sequence platform <br />
|license=site license<br />
|fields=bioinformatics<br />
}}<br />
SOLiD [http://solidsoftwaretools.com/ {{PAGENAME}}] Bioscope provides a command line for running application-specific sequence analysis tools. The Bioscope framework enables the user to perform off-instrument secondary and tertiary analyses, and it allows configurable bioinformatics workflows for resequencing (mapping, SNP finding (diBayes), copy number variations, inversions, small indels, large indels) and whole transcriptome analysis (mapping, counting, novel transcript finding, UCSC WIG Files creation) Results will be in GFF v3 and SAM formats. The resulting industry-standard files from Bioscope can be used with third-party visualization and analysis software tools.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
On UPPMAX/UPPNEX you find bioscope in the module systems on the Kalkyl cluster. <br />
<br />
Please type :<br />
module load bioinfo-tools bioscope<br />
To load the module. the command is then <br />
bioscope.sh -A b2010999<br />
To run on Kalkyl you need to specify what project shall be accounted for your job run.<br />
Bioscope integrates to the SLURM queueing system there so you only need to start bioscope.sh on a login node.<br />
We recommend you run it in the background by using "noup" <br />
nohup ./run.sh MatoBam_nohup.out<br />
Where run.sh have the run line bioscope.sh -A b2010999 -l MaToBam.log MaToBam.plan<br />
<br />
Nohup will run the job in the background and you can monitor the progress by reading the MatoBam_nohup.out.<br />
<br />
Bioscope can today use at the most 11 nodes for one bioscope run, and you can at the most start two parallel runs. This is due to the limit in the SLURM system. If you need to run several different bioscope runs. I recommend you running them one after another. <br />
<br />
Find attached the user manual to this post you need to be loged in on a registered account to read the attachment..<br />
<br />
You can also find some test data on the system under the folder:<br />
<br />
/bubo/nobackup/uppnex/bioscopedata<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://solidsoftwaretools.com/ Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BioPython&diff=2870BioPython2011-09-30T08:39:41Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=A set of freely available tools for biological computation written in Python by an international team of developers. |license=free |fields=..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A set of freely available tools for biological computation written in Python by an international team of developers.<br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://biopython.org/ {{PAGENAME}}] is a set of freely available tools for biological computation written in Python by an international team of developers.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
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== Tips and tricks ==<br />
* ...<br />
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== License ==<br />
{{show license}}<br />
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== Experts ==<br />
{{list experts}}<br />
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== Links ==<br />
* [http://biopython.org/ Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BioPerl&diff=2869BioPerl2011-09-30T08:37:25Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A community effort to produce Perl code which is useful in biology.<br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://www.bioperl.org/wiki/Main_Page {{PAGENAME}}] is a community effort to produce Perl code which is useful in biology.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.bioperl.org/wiki/Main_Page Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BioPerl&diff=2868BioPerl2011-09-30T08:37:02Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=A community effort to produce Perl code which is useful in biology. |license=free |fields=semicolon separated list of field category names ..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A community effort to produce Perl code which is useful in biology.<br />
|license=free<br />
|fields=semicolon separated list of field category names (newlines are ignored)<br />
}}<br />
[http://www.bioperl.org/wiki/Main_Page {{PAGENAME}}] is a community effort to produce Perl code which is useful in biology.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
Any further license particularities (such as site licenses) are succinctly described here.<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.bioperl.org/wiki/Main_Page Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BclConverter&diff=2867BclConverter2011-09-30T08:35:15Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Converts bcl files to Qseq files. |license=free |fields=bioinformatics }} [http://www.illumina.com/index.ilmn {{PAGENAME}}] is a converter ..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Converts bcl files to Qseq files.<br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://www.illumina.com/index.ilmn {{PAGENAME}}] is a converter program that converts bcl files to Qseq files.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.illumina.com/index.ilmn Official website]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BWA&diff=2866BWA2011-09-30T08:33:04Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=A fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target). <br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://bio-bwa.sourceforge.net/ {{PAGENAME}}] is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target). <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://bio-bwa.sourceforge.net/ Official website]<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/19451168 Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BWA&diff=2865BWA2011-09-30T08:32:51Z<p>Samuel Lampa (UPPMAX): Created page with "{{software info |description=A fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target). |license=free |fields=bioinformatics }}..."</p>
<hr />
<div>{{software info<br />
|description=A fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target). <br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://bio-bwa.sourceforge.net/ {{PAGENAME}}] is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target). <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://bio-bwa.sourceforge.net/ Official website]<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/19451168 Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BLAT&diff=2864BLAT2011-09-30T08:30:06Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=an alignment tool like BLAST, but it is structured differently. <br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://users.soe.ucsc.edu/~kent/ {{PAGENAME}}] is an alignment tool like BLAST, but it is structured differently. <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://users.soe.ucsc.edu/~kent/ Official website]<br />
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/?tool=pubmed Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BLAT&diff=2863BLAT2011-09-30T08:29:52Z<p>Samuel Lampa (UPPMAX): Created page with "{{software info |description=an alignment tool like BLAST, but it is structured differently. |license=free |fields=bioinformatics }} [http://users.soe.ucsc.edu/~kent/ {{PAGENAME..."</p>
<hr />
<div>{{software info<br />
|description=an alignment tool like BLAST, but it is structured differently. <br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://users.soe.ucsc.edu/~kent/ {{PAGENAME}}] is an alignment tool like BLAST, but it is structured differently. <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://users.soe.ucsc.edu/~kent/ Official website]<br />
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/?tool=pubmed Publication]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=BEDTools&diff=2862BEDTools2011-09-30T08:27:37Z<p>Samuel Lampa (UPPMAX): Created page with "{{software info |description=BEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature..."</p>
<hr />
<div>{{software info<br />
|description=BEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format<br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://code.google.com/p/bedtools/ {{PAGENAME}}] is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://code.google.com/p/bedtools/ Official website]<br />
* [http://bioinformatics.oxfordjournals.org/content/26/6/841.long Publication]<br />
* [http://code.google.com/p/bedtools/wiki/Usage Manual]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=ANNOVAR&diff=2861ANNOVAR2011-09-30T08:24:52Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Functional annotation of genetic variants from high-throughput sequencing data <br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://www.openbioinformatics.org/annovar/ ANNOVAR] is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform:<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.openbioinformatics.org/annovar/ Website]<br />
* [http://nar.oxfordjournals.org/content/38/16/e164 Publication]<br />
* [http://www.openbioinformatics.org/annovar/annovar_startup.html Manual]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Ab_wtp&diff=2860Ab wtp2011-09-30T08:24:43Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>{{software info<br />
|description=Alignment tool for SOLiD transcript reads <br />
|license=free<br />
|fields=bioinformatics<br />
}}<br />
[http://solidsoftwaretools.com/gf/project/transcriptome/ {{PAGENAME}}] is an alignment tool for SOLiD transcript reads <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
*...<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://pingu.com Official website]<br />
* [http://pingu.com Publication]<br />
* [http://solidsoftwaretools.com/gf/project/transcriptome/docman/?subdir=43 Manual]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Ab_wtp&diff=2859Ab wtp2011-09-30T08:17:19Z<p>Samuel Lampa (UPPMAX): Created page with "{{software info |description=Alignment tool for SOLiD transcript reads |license=free |fields=semicolon separated list of field category names (newlines are ignored) }} [http://s..."</p>
<hr />
<div>{{software info<br />
|description=Alignment tool for SOLiD transcript reads <br />
|license=free<br />
|fields=semicolon separated list of field category names (newlines are ignored)<br />
}}<br />
[http://solidsoftwaretools.com/gf/project/transcriptome/ {{PAGENAME}}] is an alignment tool for SOLiD transcript reads <br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
*...<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://pingu.com Official website]<br />
* [http://pingu.com Publication]<br />
* [http://solidsoftwaretools.com/gf/project/transcriptome/docman/?subdir=43 Manual]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=ANNOVAR&diff=2858ANNOVAR2011-09-30T08:14:23Z<p>Samuel Lampa (UPPMAX): Created page with "__NOTOC__ {{software info |description=Functional annotation of genetic variants from high-throughput sequencing data |license=free |fields= }} [http://www.openbioinformatics.or..."</p>
<hr />
<div>__NOTOC__<br />
{{software info<br />
|description=Functional annotation of genetic variants from high-throughput sequencing data <br />
|license=free<br />
|fields=<br />
}}<br />
[http://www.openbioinformatics.org/annovar/ ANNOVAR] is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform:<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
* ...<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.openbioinformatics.org/annovar/ Website]<br />
* [http://nar.oxfordjournals.org/content/38/16/e164 Publication]<br />
* [http://www.openbioinformatics.org/annovar/annovar_startup.html Manual]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Kalkyl&diff=2856Kalkyl2011-09-29T14:35:06Z<p>Samuel Lampa (UPPMAX): Undo revision 2854 by Samuel Lampa (UPPMAX) (talk)</p>
<hr />
<div>{{resource info<br />
|description=cluster resource of about 21 TFLOPS<br />
|centre=UPPMAX<br />
|software=Gaussian,ABySS,ab_wtp,ANFO,ANNOVAR,BclConverter,BEDTools,BioPerl,BioPython,bioscope,BLAST,BLAT,Bowtie,BWA,CASAVA,Concaterpillar,Cufflinks,EMBOSS,EMMAX,FastQC,FASTX,FreeBayes,GARLI,GATK,GCTA,GenomeTools,HMMER,Maq,matrix2png,MIRA,MOSAIK,mpiblast,MrBayes,MUMmer,Picard,RAxML,Ray,SAMtools,SOAPdenovo,SolexaQA,SplitSeek,Staden,Tophat,UNAFold,Velvet<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.uppmax.uu.se/systems/kalkyl Description of Kalkyl at UPPMAX web page]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=Kalkyl&diff=2854Kalkyl2011-09-29T14:33:35Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>{{resource info<br />
|description=cluster resource of about 21 TFLOPS<br />
|centre=UPPMAX<br />
|software=PGI,OpenMPI,GCC,Intel,Turbomole,GAMESS,VASP,MOLCAS,GROMACS,Desmond,Matlab,R,Gaussian,ABySS,ab_wtp,ANFO,ANNOVAR,BclConverter,BEDTools,BioPerl,BioPython,bioscope,BLAST,BLAT,Bowtie,BWA,CASAVA,Concaterpillar,Cufflinks,EMBOSS,EMMAX,FastQC,FASTX,FreeBayes,GARLI,GATK,GCTA,GenomeTools,HMMER,Maq,matrix2png,MIRA,MOSAIK,mpiblast,MrBayes,MUMmer,Picard,RAxML,Ray,SAMtools,SOAPdenovo,SolexaQA,SplitSeek,Staden,Tophat,UNAFold,Velvet<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.uppmax.uu.se/systems/kalkyl Description of Kalkyl at UPPMAX web page]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=File:Samuel.png&diff=2852File:Samuel.png2011-09-29T14:10:45Z<p>Samuel Lampa (UPPMAX): uploaded a new version of &quot;File:Samuel.png&quot;</p>
<hr />
<div></div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=User:Samuel_Lampa_(UPPMAX)&diff=2851User:Samuel Lampa (UPPMAX)2011-09-29T14:07:49Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div>{{application expert info<br />
|first name=Samuel<br />
|last name=Lampa<br />
|centre=UPPMAX<br />
|fields=Bioinformatics<br />
|fte=100<br />
|financing=SciLifeLab (50%), UPPMAX (25%), SweStore (25%)<br />
|general activities=Development of automated data handling for NextGen Sequencing data, and graphical interfaces to HPC systems.<br />
|other activities=<br />
|image=Samuel.png<br />
|office=Room 4109, House 4, Lägerhyddsvägen 2, Uppsala Universitet; SE-751 05 Uppsala<br />
|phone=+46(0)18-471 1060 (office); +46(0)70 207 3732 (mobile) <br />
}}<br />
<br />
== Quick facts ==<br />
* M.Sc. in Biotechnology in Oct 2010 (Specialization courses and degree project in Bioinformatics/Systems biology).<br />
* Working as a "close-to-the systems" Application expert at UPPMAX since October 2010 (main focus on development projects).<br />
<br />
== Expertise ==<br />
* [[expertise::Python]]<br />
* [[expertise::Java]]<br />
* [[expertise::PHP]]<br />
* [[expertise::MySQL]]<br />
* [[expertise::Mediawiki]]<br />
* [[expertise::Semantic mediawiki]]</div>Samuel Lampa (UPPMAX)https://snicdocs.nsc.liu.se/w/index.php?title=File:Samuel.png&diff=2850File:Samuel.png2011-09-29T14:06:43Z<p>Samuel Lampa (UPPMAX): </p>
<hr />
<div></div>Samuel Lampa (UPPMAX)