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--- namespace:cluster_soroban [2020/11/11 07:59]
admin
+++ namespace:cluster_soroban [2020/11/11 09:24] (current)
admin
@@ Line 11: / Line 11: @@
   - Conocimientos básicos de Linux y su linea de comando (CLI)
-===== Herramientas =====
+=====   =====
+===== Aplicaciones disponibles en Soroban (system) =====
+Compiladores, interpretes, librerias, y utilidades
+----
+índice : A|B|C|D|E|F|G|H|I|J|K|L|M|N|[[:o|O]]|P|Q|R|S|T|U|V|W|X|Y|Z
+----
+^ ^Software^Versión^Descripción|
+|**A** | | | |
+| |Anaconda python|3.7.8|Interprete python optimizado|
+|**B** | | | |
+|**C** |cmake|3.15.4|Utilidad para compilar en Linux|
+|**D** | | | |
+|**E** | | | |
+|**F** | | | |
+|**G** | | | |
+| |GCC|8.3.1|Compilador c/c++/fortran|
+| |GCC|5.5.5|Compilador c/c++/fortran|
+| |Go|1.15.2|Compilador de Lenguaje GO|
+| |Clang|3.4.2|Compilador c/c++ de LLVM|
+|**H** | | | |
+| |HDF5|1.10.5|FileSystem Distribuido|
+|**I** | | | |
+|**J** | | | |
+| |Java Develop Kit (JDK)|11.0.8|JDK (openjdk) librerias/compilador JAVA|
+|**K** | | | |
+|**L** | | | |
+|**M** | | | |
+| |Math Kernel Library (MKL)|2018.4-274|Librerias matemáticas optimizadas de Intel|
+|**N** | | | |
+|**O** | | | |
+| |openmpi|1.10.7|Programación paralela|
+| |openmpi|3.1.5|Programación paralela|
+| |openmpi|1.6.5|Programación paralela|
+| |openmpi|2.1.6|Programación paralela|
+| |openblas|3.3-2|Implementación opensource de BLAS y LAPACK ; algebra lineal|
+|**P** | | | |
+| |Perl|5.16.3|Interprete del lenguaje Perl|
+|**Q** | | | |
+|**R** | | | |
+|**S** | | | |
+|**T** | | | |
+|**U** | | | |
+|**V** | | | |
+|**W** | | | |
+|**X** | | | |
+|**Y** | | | |
+|**Z** | | | |
+====== Aplicaciones Científicas ======
+Bioinformatics, Chemistry, Physics, etc
+índice : A|B|C|D|E|F|G|H|I|J|K|L|M|N|O|P|Q|R|S|T|U|W|X|Y|Z
+----
+| \\ **#** | \\ **Aplicación** | \\ **Versión** | \\ **Descripción** |
+|**A** | | | |
+| |aragorn|1.2.38|tRNA (and tmRNA) detection|
+| |arb|6.0.6|Phylogenetic analysis of rRNA and other biological sequences such as amino acids|
+| |ascp|3.9.9|–|
+|**B** | | | |
+| |bowtie2|0.7.17|software package for mapping low-divergent sequences against a large reference genome, such as the human genome|
+| |bwa|2.4.1|alineación de secuencias y el análisis de secuencias en bioinformática|
+| |blast+|2.9.0|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas|
+| |blast+|2.10.0(default)|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas|
+| |blast|2.2.26|Alineamiento de secuencias de tipo local, ya sea de ADN, ARN o de proteínas|
+| |bedtools|2.29.2|swiss-army knife of tools for a wide-range of genomics analysis tasks|
+| |bedops|2.4.38|highly scalable and easily-parallelizable genome analysis toolkit|
+| |beagle-lib|3.1.2|high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics|
+| |bcftools|1.10.2|set of utilities that manipulate variant calls|
+| |bbtools|38.86|suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data|
+| |barrnap|0.9|predicts the location of ribosomal RNA genes in genomes|
+| |bamtools|2.5.1|toolkit for handling BAM files.|
+| | | | |
+|**C** | | | |
+| |cufflinks|2.10|finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads|
+| |circos|2.2.1|Transcriptome assembly and differential expression analysis for RNA-Seq.|
+| |cutadapt|0.69-9|for visualizing data and information. It visualizes data in a circular layout|
+| |checkm|1.1.2|set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes|
+| |cdhit|4.8.1|Takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr)…|
+| |canu|1.9|Fork of the Celera Assembler designed for high-noise single-molecule sequencing|
+| | | | |
+| | | | |
+|**D** | | | |
+| |diamond|0.9.35|molecular and crystal structure visualization software|
+|**E** | | | |
+|**F** | | | |
+|**G** | | | |
+| |gromacs|2019.4|Modelamiento Molecular|
+|**H** | | | |
+| |hmmer|2.3.2|biosequence analysis using profile hidden Markov models .|
+| |hmmer|3.1b1|biosequence analysis using profile hidden Markov models .|
+| |hmmer|3.1b2|biosequence analysis using profile hidden Markov models .|
+| |hmmer|3.2.1|biosequence analysis using profile hidden Markov models .|
+| | | | |
+|**I** | | | |
+|**J** | | | |
+|**K** | | | |
+|**L** | | | |
+|**M** | | | |
+|**N** | | | |
+| |Namd2|2019-11-27-multicore|Modelamiento Molecular|
+|**P** | | | |
+|**Q** | | | |
+|**R** | | | |
+| |R|3.6.1|Analísis Estadistico|
+| | | | |
+|**W** | | | |
+| |WRF|3.9.1|Mesoscale numerical weather prediction|
+| |WRF|4.0|Mesoscale numerical weather prediction|
+|**X** | | | |
+| \\ **6** | \\ netcdf/c| \\ 4.7.3| \\ Network Common Data Form|
+| \\ **7** | \\ netcdf/fortran| \\ 4.5.2| \\ Network Common Data Form|
+| \\ **8** | \\ quantum-espresso/schrodinger| \\ 6.4.1-2019-4| \\ Modelamiento Molecular|
+| \\ **32** | \\ eggnog-mapper| \\ 2.0.1| \\ tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters|
+| \\ **33** | \\ EMBOSS| \\ 6.6.0| \\ European Molecular Biology Open Software Suite|
+| \\ **34** | \\ FastANI| \\ 1.3| \\ Produces accurate ANI estimates and is faster than alignment (e.g., BLAST)- based approaches.|
+| \\ **35** | \\ vcftools| \\ 0.1.17| \\ package designed for working with VCF files|
+| \\ **36** | \\ Unicycler| \\ 0.4.9b| \\ assembly pipeline for bacterial genomes|
+| \\ **37** | \\ tRNAscan-SE| \\ 2.0.5| \\ searches for tRNA genes in genomic sequences|
+| \\ **38** | \\ trinityrnaseq| \\ 2.11.0| \\ Trinity RNA-Seq de novo transcriptome assembly|
+| \\ **39** | \\ trf| \\ 4.09| \\ Analyze DNA sequences|
+| \\ **40** | \\ TransDecoder| \\ 5.5.0| \\ Assist in the identification of potential coding regions within ….|
+| \\ **41** | \\ tophat| \\ 2.1.1| \\ Alineación del rendimiento de las lecturas de secuenciación de cDNA …|
+| \\ **42** | \\ tbl2asn| \\ 3.10.0| \\ Automates the creation of sequence records for submission to GenBank|
+| \\ **43** | \\ ssu-align| \\ 0.1.1| \\ identifying, aligning, masking and visualizing archaeal 16S, bacterial 16S and eukaryotic 18S…|
+| \\ **44** | \\ sratoolkit| \\ 2.10.7| \\ Using the SRA Toolkit to convert .sra files into other formats …|
+| \\ **45** | \\ SPAdes| \\ 3.14.1| \\ Assembly toolkit containing various assembly pipelines.|
+| \\ **46** | \\ SPAdes| \\ 3.13.2| \\ Assembly toolkit containing various assembly pipelines.|
+| \\ **47** | \\ SINA| \\ 1.6.1| \\ accurate high-throughput multiple sequence alignment of ribosomal RNA genes.|
+| \\ **48** | \\ seqtk| \\ 1.3| \\ A fast and lightweight tool for processing sequences in the FASTA or FASTQ format.|
+| \\ **49** | \\ seqkit| \\ 0.12.1| \\ Seqkit is a tool for manipulating fasta and fastq files.|
+| \\ **50** | \\ samtools| \\ 1.10.2| \\ suite of programs for interacting with high-throughput sequencing data|
+| \\ **51** | \\ salmon| \\ 1.2.1| \\ Is a tool for quantifying the expression of transcripts using RNA-seq data.|
+| \\ **52** | \\ RSEM| \\ 1.3.3| \\ Tool for the quantification of RNA-seq data.|
+| \\ **53** | \\ roary| \\ 1.7.7| \\ Application for rapidly constructing pan genomes from large numbers of prokaryote sample|
+| \\ **54** | \\ racon| \\ 1.4.16| \\ Consensus sequence|
+| \\ **55** | \\ quast| \\ 5.1.0rc1| \\ Quality Assessment Tool for Genome Assemblies|
+| \\ **56** | \\ pyani| \\ 0.2.10| \\ a Python3 module that provides support for calculating average nucleotide identity (ANI)|
+| \\ **57** | \\ prokka| \\ 1.14.6| \\ tool for the rapid annotation of prokaryotic genomes|
+| \\ **58** | \\ prodigal| \\ 2.6.3| \\ Prodigal is an unsupervised machine learning algorithm|
+| \\ **59** | \\ prinseq| \\ 0.20.4| \\ Tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim …|
+| \\ **60** | \\ prank| \\ 170427| \\ Is a probabilistic multiple alignment program for DNA,|
+| \\ **61** | \\ pplacer| \\ 1.1.alpha17| \\ Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference …|
+| \\ **62** | \\ htslib| \\ 1.10.2| \\ An implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, …|
+| \\ **63** | \\ mash| \\ 2.2| \\ Reduces large sequences and sequence sets to small, …|
+| \\ **64** | \\ mafft| \\ 7.470| \\ is a multiple sequence alignment program for unix-like operating systems|
+| \\ **65** | \\ ksnp| \\ 3.1.2| \\ Finds single nucleotide polymorphisms (SNPs) in whole genome data.|
+| \\ **66** | \\ krona| \\ 2.7.1| \\ powerful metagenomic visualization tool|
+| \\ **67** | \\ kaiju| \\ 1.7.3| \\ program for the taxonomic classification of high-throughput sequencing reads.|
+| \\ **68** | \\ jellyfish| \\ 2.3.0| \\ tool for fast, memory-efficient counting of k-mers in DNA.|
+| \\ **69** | \\ jdk| \\ 8.0_41| \\ Java Develop ToolKit|
+| \\ **70** | \\ jdk| \\ 14.0.1| \\ Java Develop ToolKit|
+| \\ **71** | \\ jdk| \\ 11.28| \\ Java Develop ToolKit|
+| \\ **72** | \\ infernal| \\ 1.1.3| \\ for searching DNA sequence databases for RNA structure and sequence similarities|
+| \\ **73** | \\ pilon| \\ 1.23| \\ an automated genome assembly improvement and variant detection tool|
+| \\ **74** | \\ picard| \\ 2.23.1| \\ a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.|
+| \\ **75** | \\ phyml| \\ 3.3.20190909| \\ is a phylogeny software based on the maximum-likelihood principle|
+| \\ **76** | \\ phylip| \\ 3.697| \\ a free package of programs for inferring phylogenies|
+| \\ **77** | \\ parallel| \\ 20200622| \\ Parallel is an indispensible tool for speeding up bioinformatics. It allows you to easily parallelize commands|
+| \\ **78** | \\ paml| \\ 4.9| \\ a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.|
+| \\ **79** | \\ ncftp| \\ 3.2.6| \\ cliente ftp|
+| \\ **80** | \\ muscle| \\ 3.8.31| \\ A program to create multiple sequence alignments of a large number of sequences|
+| \\ **81** | \\ MUMmer| \\ 3.23| \\ an open source software package for the rapid alignment of very large DNA and amino acid sequences|
+| \\ **82** | \\ mothur| \\ 1.44.1| \\ a single resource to analyze molecular data that is used by microbial ecologists|
+| \\ **83** | \\ minimap2| \\ 2.17| \\ pairwise alignment for nucleotide sequences.|
+| \\ **84** | \\ miniconda| \\ 4.8.3| \\ python minimalist|
+| \\ **85** | \\ MCL| \\ 14-137| \\ a cluster algorithm for graphs|
+| \\ **86** | \\ MinCED| \\ 0.4.2| \\ program to find Clustered Regularly Interspaced Short .|
+| \\ **87** | \\ fastqc| \\ 0.11.9| \\ a quality control application for high throughput sequence data.|
+| \\ **88** | \\ fasttree| \\ 2.1.11| \\ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences|
+| \\ **89** | \\ Gblocks| \\ 0.91b| \\ computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein|
+| \\ **90** | \\ go| \\ 1.14.4| \\ compilador de lenguaje GO|
+| \\ **91** | \\ gtdbtk| \\ 1.2.0| \\ a toolkit to classify genomes with the Genome Taxonomy Database, B|
 ====== Activación de MFA (opcional) ======
-<font 16px/inherit;;inherit;;inherit>Multi Factor Authenticator (MFA) . Este método agrega un capa de seguridad extra a las cuentas de los investigadores, y es obligatorio para todos los usuarios.</font>
+<font 16px/inherit;;inherit;;inherit>Multi Factor Authenticator (MFA) . Este método agrega un capa de seguridad extra a las cuentas de los investigadores, <del>y es obligatorio para todos los usuarios.</del></font>
 <font 16px/inherit;;inherit;;inherit>Para activar y usar MFA es necesario seguir tres simples pasos descritos a continuación:</font>
@@ Line 177: / Line 357: @@
 <font 16px/inherit;;inherit;;inherit>En situaciones especiales como perdida, daño, desinstalación o simplemente cambio de smartphone estan disponibles varias alternativas:</font>
-  - <font 16px/inherit;;inherit;;inherit>Utilizar uno de los 5 códigos de emergencias descritos en el paso 3 para accesar cuando google authenticator no este disponible. Eliminar el archivo .google_authenticator en tu cuenta en Soroban ejecutando el siguiente comando: rm -rf .google_authenticator , y luego repetir el paso 3.</font>- - <font 16px/inherit;;inherit;;inherit>Ingresar el actual secret key directamente en la nueva instalación de google authenticator en el smartphone para volver activar MFA.</font>- - <font 16px/inherit;;inherit;;inherit>Contactar como último recurso al siguiente correo en cualquier horario para soporte : raphael.verdugo@ufrontera.cl</font>
+  - <font 16px/inherit;;inherit;;inherit>Utilizar uno de los 5 códigos de emergencias descritos en el paso 3 para accesar cuando google authenticator no este disponible. Eliminar el archivo .google_authenticator en tu cuenta en Soroban ejecutando el siguiente comando: rm -rf .google_authenticator , y luego repetir el paso 3.</font>-
+  - - <font 16px/inherit;;inherit;;inherit>Ingresar el actual secret key directamente en la nueva instalación de google authenticator en el smartphone para volver activar MFA.</font>- -
+  - <font 16px/inherit;;inherit;;inherit>Contactar como último recurso al siguiente correo en cualquier horario para soporte : raphael.verdugo@ufrontera.cl</font>
+======   ======
+====== Primeros pasos en Soroban ======
+[[:namespace:iniciar_session_en_soroban|iniciar session en Soroban]]
+[[:namespace:cargar_un_software_en_soroban|Cargar un software en Soroban]]
+[[:namespace:ejecutar_un_trabajo_en_soroban|Ejecutar un trabajo en Soroban]]
+====== Cargando un software/libreria en Soroban ======
 ====== Utilización de module ======
@@ Line 198: / Line 392: @@
 <font 16px/inherit;;inherit;;inherit>El ejemplo contiene los comandos necesarios para :</font>
-  - <font 16px/inherit;;inherit;;inherit>Listar las aplicaciones disponibles</font>- <font 16px/inherit;;inherit;;inherit>Cargar los programas/librerias deseados</font>- <font 16px/inherit;;inherit;;inherit>Verificar que este disponible la libreria/aplicación que se ha cargado</font>- <font 16px/inherit;;inherit;;inherit>Descargar las aplicaciones cuando no sean necesarias o se desee otra versión.</font>
+  - Listar las aplicaciones disponibles.
+  - Cargar los programas/librerias deseados.
+  - Verificar que este disponible la libreria/aplicación que se ha cargado.
+  - Descargar las aplicaciones cuando no sean necesarias o se desee otra versión.
-{{:namespace:module4-c.png?nolink&1500x679}}
+  - {{:namespace:module4-c.png?nolink&1500x679}}
 ======   ======