New Home!,,url "

By your requests we implemented new style home pages, for your convenience. The new portal should look and feel what many of you called Outlook style or Explorer style: project based folders you create on the left, lists of objects on the top right, and the content on the bottom right.

The older home page interface is temporarily available by clicking this notification message. As soon as we migrate all of the tools to the new interface, we make sure that you like it and it sticks, the older home page will be depreciated and discontinued.

We are aware that just like anything else new, some issues may come up, some problems may appear while using the new system. We are working hard to fix those ! But we wanted you to know that we invite your comments. Please, report ANY problems you see. We know that you, our users play an important and critical role in creating HIVE, we appreciate every step, any recommendation, an inquiry and a desire to make HIVE better.

When you talk, we listen!

Please, use the new Home Pages! Enjoy the new interface!.

HIVE Portal
img/bio-project.gif,record&types=HIVE_Project,,HIVE project,Create a new project     
img/bio-sample.gif,record&types=HIVE_Sample,,HIVE sample,Create a new sample,RecordsSample
img/bio-experiment.gif,record&types=HIVE_Experiment,,HIVE experiment, Create a new experiment
img/bio-run.gif,record&types=HIVE_Run,,HIVE run,Create a new run
img/list.gif,record&types=Hive_Development_Project_List,,HIVE user project list, Create a new project list object 
icon,name,mode,title,description img/bio-sample.gif,record&types=HIVE_Sample,,HIVE sample,Create a basic sample img/bio-sample.gif,record&types=hive-sample-animal,,HIVE animal sample,Create an animal or human sample
img/rec.gif,tblqry-new,,Table Query, This tool takes you to the table query utility
img/hiveseq.gif,dna-hiveseq,, Hive-Seq, Page that allows users to have access to all hive seq utilities
img/random.png,dna-insilico,,Genome Randomizer,Next-Gen Sequence Randomizer (dna-insilico) 
img/seqtrim.png,dna-hiveseq,seqtrim,Sequence Trimmer, Allows users to trim sequences based on specific parameters
img/filter.png,dna-hiveseq,primersfilter, Primers Filter, Tool to generate sequences while taking primers into consideration
img/dna.gif,dna-hiveseq,adaptersfilter, Adapters Filter, Tool to generate sequences while taking adapters into consideration
img/length.png,dna-hiveseq,qualityandlengthfilter, Quality and Length Filter, Tool to filter results based on their quality and length
img/hive-hexagon.gif,dna-multi-qc,,Multiple QC,Quality control across multiple short read files.
img/graph.gif,dna-hiveseq,complexityfilter, Complexity Filter, Tool to filter low complexity regions
img/graph.gif,dna-hiveseq,idfilter, Identification Filter, Tool to filter Identification lines from a file
img-algo/genome.jpg,dna-hiveseq,seqfilter, Sequence Filter, Tool to filter sequences from a file
img/graph.gif,dna-hiveseq,pairedEndCollapse, Paired End Collapser, Tool to collapse two paired end files into one
img/random.png,dna-hiveseq,randomizer,Simulated Random Sequence Generation,Choose this to discover recombination sites in population of genomes    
img/hiveseq.jpg,dna-hiveseq,vioseq, Sequence Combining Tool, Tool allowing creation of hive-seq virtual sequence files by combining the sequences and ranges from other sequence files.
img-algo/sfat.png,dmStrDistri,,Sequence Feature Analysis Tool, Collection of tools which allow to compute proteomic analysis.
img/hiveseq.jpg,geneExpression,,Gene Expression Analysis Portal, Portal allowing to analyze measurements from gene expression experiments .
img-algo/svc-protein-rosetta_scripts.png,rosetta,,Rosetta Scripts,Rosetta is a suite of software libraries for macromolecular modeling. An xml-based scripting language for control of modeling trajectories.
icon,name,mode,aligner,<!--section-->type,Metagenomic-seq algorithms,description
img/scope.png,dna-screening,,,dna,Censuscope,Choose this option to rapidly define the taxonomic composition in a metagenomic sequence dataset
img/scope.png,dna-pipeline-pathoscope,,,dna,Pathoscope:Beta Testing,Choose this option for species identification and strain attribution with unassembled sequencing data developed by Crandall group at GWU 

icon,name,mode,aligner,<!--section-->type,DNA-seq algorithms,description
img/hive-hexagon.gif,dna-hexagon-menu,,HIVE-Hexagon,dna,HIVE-Hexagon Menu,Choose this option to view the general and subject specific HIVE hexagon pages used to align sequence reads to a reference genomes using the HIVE-Hexagon native engine
img/hive-hexagon.gif,dna-hexagon-menu,test,HIVE-Hexagon-test,dna,Test HIVE-Hexagon Menu,Choose this option to view the general and subject specific HIVE hexagon pages used to align sequence reads to a reference genomes using the HIVE-Hexagon native engine
img-algo/svc-align-blast.gif,dna-hexagon-menu,blast,Blast,dna,BLAST Alignment Menu,Choose this to align sequence reads to reference genomes using integrated NCBI BLAST
img-algo/svc-align-blast.gif,dna-hexagon-menu,blastx,BlastX,dna,BLASTX Alignment Menu,Choose this to align sequence reads to protein reference genomes using integrated NCBI BLASTX
img-algo/svc-align-blast.gif,dna-hexagon-menu,tblastx,TBlastX,dna,TBLASTX Alignment Menu,Choose this to align sequence reads to reference genomes using integrated NCBI TBLASTX
img-algo/svc-align-bowtie.gif,dna-hexagon-menu,bowtie,Bowtie,dna,Bowtie Alignment Menu,Choose this to align sequence reads to a reference genomes using Bow-tie
img-algo/svc-align-bwa.gif,dna-hexagon-menu,bwa,BWA,dna,BWA alignment Menu, Choose this to align sequence reads to a reference genomes using BWA
img-algo/svc-align-blat.gif,dna-hexagon,blat,BLAT,,BLAT, Choose this to access BLAT alignment as development by UCSC
img/dna.gif,dna-hexagon&cmdMode=batch,,HIVE-Hexagon,dna,DNA Batch,Batch mode for DNA hexagon
,,,,<!--section-->,RNA-seq algorithms,description

img-algo/svc-align-hisat2.gif,dna-hexagon-menu,hisat2,HISAT2,rna,HISAT2 RNA alignment Menu, Choose this to align RNA sequence reads to reference genome using HISAT2
img-algo/svc-align-tophat.gif,dna-hexagon-menu,tophat,Tophat,rna,Tophat RNA alignment Menu, Choose this to align RNA sequence reads to reference genome using Tophat
,,,,<!--section-->,multiple alignment algorithms,description
img-algo/svc-align-mafft.gif,dna-hexagon,mafft,MAFFT,dna,MAFFT multiple alignment Menu, Choose this to align multiple sequence reads to each other using MAFFT
img-algo/svc-align-clustal.gif,dna-hexagon,clustal,Clustal,dna,Clustal multiple alignment Menu, Choose this to align multiple sequence reads to each other using Clustal
,,,,<!--section-->,post-alignment algorithms,description
img/hive-hexagon.gif,dna-alignment-comparator,postal,Alignment Comparator,dna,Alignment comparison algorithm, Choose this to compare multiple alignments  
img-algo/hive-population.gif,dna-popul,,QSR tool,postal,Hexahedron algorithm, Choose this to resolve genetic diversity in NGS samples
img/table.gif,dna-tnseq,,,,Tn-Seq,Format alignments into unified Tn-Seq table  
img/hiveseq.jpg,dna-pipeline-idba-ud,,HIVE Small Genome de Novo Assembly (with IDBA-UD), Tool used for small genome Sequence Assembly using IDBA-UD software
img/hiveseq.jpg,dna-pipeline-velvet-single,,HIVE Small Genome de Novo Assembly (with Velvet), Tool used for small genome Sequence Assembly using Velvet software
img/hiveseq.jpg,dna-price,,HIVE Small Viral Genome de Novo Assembly (with PRICE), Tool used for small genome Sequence Assembly using PRICE software
img/hiveseq.jpg,dna-hiveseq,hs-contigextension,Contig Extension, Tool used to build contigs from short Reads
img-algo/svc-annotation-converter.png,annotationConverter&cmdMode=iondb,,Annotation Converter,"This tool allows converts CSV, TSV, VCF, and GTF files into HIVE Annotation Objects for use with other HIVE tools."
img-algo/svc-annotation-mapper.gif,annotationMapper&cmdMode=iondb,,Annotation Mapper, This tool allows you to crossmap two or more profiles or annotations to discover similarities and differences between them.
img/hiveseq.jpg,dna-genemark,,GeneMark, This tool accepts a Nucleotide sequence file and annotates it using BLASTP and NR.

img-algo/svc-annotation-converter.png,dna-pipeline-macs-callpeaks,,MACS2 Callpeak,"Integration of MACS2 Callpeak peak calling tool into HIVE."
img-algo/svc-annotation-converter.png,dna-pipeline-macs-bdgcmp,,MACS2 BDGCMP Function,"Integration of MACS2 BDGMCP tool into HIVE."

img/tree.gif,taxonomy,,Taxonomy Dataset, Datasets of taxonomy information
img/treeNew.gif,algorlda,,Discriminant Classification ,Regularized linear discriminant analysis to distinguish the factors affecting transition between two classes of samples
img-algo/svc-clust.png,dna-clust,,Sequence Hierarchical Clustering,Hierarchical clustering analysis that classifies related profiling results by comparing their SNP frequencies
img/hive-hexagon.gif,textClustering,,Genotypic Variation Clustering, This tool allows Genotypic variation clusterization
img-algo/alignment_comparator.png,dna-alignment-comparator,,Alignment Comparator, This tool allows you to compare alignments
img/hive-hexagon.gif,reg_virMut,,Viral Mutation Comparator,"Comparative viral substitution analysis tool."
img-algo/mothur.png,dna-pipeline-mothur-16s,,Mothur MiSeq Pipeline,"Pipeline implementing the MiSeq SOP published by Schloss Lab for 16s ribosomal classification." 

img-algo/svc-spectraPeakDetection.jpg,spectraPeakDetection&cmdMode=special,,MS Spectra Analysis,"Collection of Mass-spec smoothing, de-noising, fourier and wavelet analysis, baselining, and peak detection algorithms."
img-algo/svc-spectraPeakDetection.jpg,glymps,,Glymps for glyco-proteomics,Glymps for glyco-proteomics
img-algo/svc-spectraPeakDetection.jpg,msgfplus,,MSGF+ for glyco-proteomics,MSGF+ for glyco-proteomics
img-algo/elisa.png,elisa,,ELISA,"Enzyme-linked immunosorbent assay suit of tools for visualization and analysis."
img/hive-hexagon.gif,renamer,,Renamer,"Rename collection of many objects here."
img/table.gif,dna-differential-profiler,,Differential Profiler,"Differential Profiler tool"

High-performance Integrated Virtual Environment (HIVE)

The Department of Biochemistry & Molecular Medicine, The School of Medicine and Health Sciences, The George Washington University, Ross Hall 530, 2300 Eye St, NW Washington, DC 20037
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