http://www.medcomp.medicina.unipd.it/main_site/ 2026-05-22T01:14:03+02:00 http://www.medcomp.medicina.unipd.it/main_site/ http://www.medcomp.medicina.unipd.it/main_site/lib/images/favicon.ico text/html 2014-02-14T11:36:27+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=advanced_options&rev=1392374187&do=diff KEESEEK ADVANCED OPTIONS WARNING: not all combinations of the following options have been tested, please use them carefully and avoid conflicting parameters and values. We do not guarantee consistency of unexpected combinations of parameters. Filters for primer-like features (see here for details) text/html 2013-04-10T11:48:06+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=arabidopsis&rev=1365587286&do=diff Arabidopsis thaliana text/html 2013-11-04T11:36:55+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=argot2results&rev=1383561415&do=diff Argot2 results for CAFA2 text/html 2014-06-04T12:41:34+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=blast&rev=1401878494&do=diff Blast text/html 2013-03-04T19:56:10+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=configurazione&rev=1362423370&do=diff Configurazione Switch * numero: 1 * modello: Extreme Summit 5i * connessioni: tutte le 12 porte disponibili (da 1 Gb/s) sono collegate, 8 agli host, 2 allo storage e le 2 rimanenti agli host “backup” e “NFSserver” Dischi * modello: Seagate ST31000340NS * numero: 16, 2 sono “spare” * configurazione: ReiserFS * taglio: 1TB * raid: RAID-10 * size: 1TB x (16 - 2) in RAID-10 => 6.1TB * tecnologia: SATA * numero di LUN (volumi) configurate: 1 Volume con due partizioni “data” … text/html 2013-03-04T19:41:33+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=dpack&rev=1362422493&do=diff DPACK Il resoconto in “backup.iokit” è stato generato mentre IOstat era eseguito solo sul server “backup”. I resoconti contenenti “all” sono stati generati mentre IOstat era eseguito su tutti i server contemporaneamente. text/html 2013-03-04T09:37:55+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=emcgrab&rev=1362386275&do=diff emcgrab text/html 2014-04-15T18:38:01+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=expected_time_to_see_the_first_results&rev=1397579881&do=diff Expected time to see the first results The larger your genome, the longer it will take for keeSeek to produce an output. A good starting point for generating primer-like neverwords is the anagram mode with an even distribution of nucleotides (-a 5:5:5:5). Nevertheless, big genomes (e.g. human genome) will require a certain amount of time to produce the first results. Some estimates for different genome sizes are reported in the following table, for both GPU and CPU versions of keeSeek. Note th… text/html 2019-07-30T09:51:07+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus&rev=1564473067&do=diff G-quadruplexes are non-canonical nucleic acid structures that control transcription, replication and translation, regulated genome recombination and genetic and epigenetic instability. G-quadruplexes are present in eukaryotes, prokaryotes and viruses. On this platform the analyses performed on all human viruses can be easily examined and downloaded. text/html 2013-04-03T16:34:25+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=genomi&rev=1364999665&do=diff Genomi disponibili * Mycobacterium tubercolosis * Arabidopsis thaliana * Homo sapiens text/html 2013-04-02T11:08:43+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=homo&rev=1364893723&do=diff Homo sapiens text/html 2013-03-04T19:41:08+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=iostat&rev=1362422468&do=diff IOstat Questi file sono stati prodotti conteporaneamente (con il comando dsh -M -c -a iostat/esegui.sh). text/html 2014-06-05T16:50:39+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=keeseek&rev=1401979839&do=diff keeSeek is a command line tool for generating, for a given reference genome, a set of k-mers absent in that genome. We call them neverwords. Downloads keeSeek requires a CPU with the SSE4 instruction set and a Nvidia graphic card. There is an option (-N) to omit GPU computations but it is not recommended, being GPGPU a strong advantage. text/html 2014-04-16T11:53:24+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=license&rev=1397642004&do=diff THE Q PUBLIC LICENSE version 1.0 Copyright (C) 1999 Troll Tech AS, Norway. Everyone is permitted to copy and distribute this license document. The intent of this license is to establish freedom to share and change the software regulated by this license under the open source model. text/html 2014-02-17T17:52:54+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=listgpus&rev=1392655974&do=diff List of tested GPUs We observed that Nvidia drivers installed from Linux repositories are either non working or slower than the official Nvidia drivers. The Linux version is compiled with the CUDA Toolkit 4 and the officially supported Linux versions are the following: text/html 2013-04-02T11:07:04+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=mycobacterium&rev=1364893624&do=diff Mycobacterium tubercolosis text/html 2018-03-15T11:09:37+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=nessie&rev=1521108577&do=diff NeSSie is a c/c++ 64 bit program that allows to perform fast patterns search and sequence analyses on DNA strings using the NeSSie library. The tool currently offers the following types of analyses: * De novo search for motifs with a mirror or palindromic symmetry, as well as motifs with a DNA-triplex forming potential. Both perfect and degenerate motifs (motifs containing gaps and mismatches) can be detected. * Exhaustive search for all k-mers in the sequence. * Calculation of the sequ… text/html 2013-03-04T19:50:56+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=performancedata&rev=1362423056&do=diff Analisi sul cluster * configurazione * dpack * iostat * emcgrab * summary text/html 2018-03-01T12:58:18+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=prova&rev=1519905498&do=diff GG islands [zika virus GG] text/html 2014-01-30T11:31:22+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=restricted&rev=1391077882&do=diff Restricted area Bugtracker http://www.medcomp.medicina.unipd.it/flyspray/ System monitor http://www.medcomp.medicina.unipd.it/backup/zabbix/ Versioning system http://www.medcomp.medicina.unipd.it/repos/ Data PerformanceData Genomi Codice text/html 2018-01-16T16:21:33+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=start&rev=1516116093&do=diff Please use the back button of your browser! text/html 2013-03-02T19:07:23+02:00 http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=summary&rev=1362247643&do=diff Number of files