class: center, middle, inverse, title-slide # Analysis of RNAseq data in R and Bioconductor (part 1)
###
http://rockefelleruniversity.github.io/RU_RNAseq/
--- ## RNAseq RNAseq offers a method to simultaneously measure the genome wide expression of annotated and novel transcripts.

 --- ## RNAseq for differential gene expression A common goal in RNAseq is to identify genes and/or transcripts which are expressed at differing levels between our user defined sample groups. Absolute quantification of the expression level of gene is subject to measurement biases (GC bias in PCR and/or RNA capture/selection) so it is most appropriate to compare the levels of the expression of same gene across conditions than to compare differing genes' expression levels within a condition. This commonly referred to as differential gene or transcript expression (DGE/DTE).

 --- ## RNAseq for differential transcript usage A less frequent but important goal in RNAseq is to identify any changes in the relative abundance of transcripts for a gene between conditions. This may be able to identify changes in a genes' functional role between conditions i.e. one isoform of a protein may bind and activate, another may simply bind and obstruct other active forms. We call this differential transcript usage (DTU).

 --- ## What we will cover * _Session 1: Alignment and counting_ * Session 2: Differential gene expression analysis * Session 3: Visualizing results through PCA and clustering * Session 4: Gene Set Analysis * Session 5: Differential Transcript Utilization analysis --- ## The data Over these sessions we will review data from Christina Leslie's lab at MSKCC on T-Reg cells. This can be found on the Encode portal. T-Reg data [here](https://www.encodeproject.org/experiments/ENCSR486LMB/) and activated T-Reg data [here](https://www.encodeproject.org/experiments/ENCSR726DNP/). --- ## The data Several intermediate files have already been made for you to use. You can download the course content from GitHub [here](https://github.com/RockefellerUniversity/RU_RNAseq/archive/master.zip). Once downloaded you will need to unzip the folder and then navigate into the *r_course* directory of the download. This will mean the paths in the code are correct. ```r setwd("Path/to/Download/RU_RNAseq-master") ``` --- class: inverse, center, middle # Working with raw RNAseq data

 --- ## Working with raw RNAseq data FASTQ data can be directly read into R with the [ShortRead package](https://bioconductor.org/packages/release/bioc/html/ShortRead.html) to review sequence data quality. We have covered how to work with raw sequencing data in the [**FASTQ in Bioconductor** session.](https://rockefelleruniversity.github.io/Bioconductor_Introduction/r_course/presentations/slides/FastQInBioconductor.html#1). Reading everything into R can take a lot of time and memory. Most times we just want to do some QC and maybe filter out low quality reads or trim. To do this in a fast or simple manner we can use the [*Rfastp*](https://bioconductor.org/packages/release/bioc/html/Rfastp.html) package. --- ## Our FASTQ file We can download the full FASTQ using this R code. ```r fq <- "https://www.encodeproject.org/files/ENCFF332KDA/@@download/ENCFF332KDA.fastq.gz" download.file(fq, "ENCFF332KDA.fastq.gz") ``` Alternatively a subset is available in the data directory: *data/ENCFF332KDA_sampled.fastq.gz* --- ## Rfastp To run QC with Rfastp, we just need to use the *rfastp()* function on our FASTQ file. We also need to provide the prefix we want for the outputs to *outputFastq*. ```r json_report <- rfastp(read1 = "data/ENCFF332KDA_sampled.fastq.gz", outputFastq = "ENCFF332KDA_rfastp") ``` --- ## Rfastp outputs Running RfastP creates several files: 1. XXX_R1.fastq.gz - FASTQ with poor quality reads filtered out 2. XXX.html - HTML file contains a QC report 3. XXX.json - JSON file with all the summary statistics ``` ## [1] "ENCFF332KDA_rfastp_R1.fastq.gz" "ENCFF332KDA_rfastp.html" ## [3] "ENCFF332KDA_rfastp.json" ``` --- ## Rfastp outputs in R The object saved in R is in json format. There are several functions that allow you to extract the information out into a more readable format such as the **qcSummary()** function. This details the Before/After stats. ```r qcSummary(json_report) ``` ``` ## Before_QC After_QC ## total_reads 1.000000e+06 9.967650e+05 ## total_bases 5.000000e+07 4.983825e+07 ## q20_bases 4.870494e+07 4.864858e+07 ## q30_bases 4.740574e+07 4.739273e+07 ## q20_rate 9.740990e-01 9.761290e-01 ## q30_rate 9.481150e-01 9.509310e-01 ## read1_mean_length 5.000000e+01 5.000000e+01 ## gc_content 4.823030e-01 4.821960e-01 ``` --- ## Rfastp - Base Quality The curvePlot function can also be used to plot specific QC aspects like base quality and GC content. ```r curvePlot(json_report) ``` ![](RU_RNAseq_p1_files/figure-html/unnamed-chunk-8-1.png) ## Rfastp - GC content ```r curvePlot(json_report, curve = "content_curves") ``` ![](RU_RNAseq_p1_files/figure-html/unnamed-chunk-9-1.png) --- ## Rfastp, trimming and more There are a lot of options for the *rfastp()* function that allow you to customize filtering, trimming and more. ```r `?`(rfastp) ``` --- class: inverse, center, middle # Aligning RNAseq data

 --- ## Aligning RNAseq reads Following assessment of read quality, we will want to align our reads to the genome taking into account splice junctions. Not all RNAseq reads will align continuously against our reference genome. Instead they will map across splice junctions, so we need to use [splice aware aligners, that we have seen in previous sessions.](https://rockefelleruniversity.github.io/Bioconductor_Introduction/r_course/presentations/slides/AlignmentInBioconductor.html#6) The resulting BAM file will contain aligned sequence reads for use in further analysis.

 --- ## Creating a reference genome First we need to retrieve the sequence information for the genome of interest in [FASTA format.](https://rockefelleruniversity.github.io/Genomic_Data/presentations/slides/GenomicsData.html#9) We can use the [BSgenome libraries to retrieve the full sequence information.](https://rockefelleruniversity.github.io/Bioconductor_Introduction/presentations/slides/SequencesInBioconductor.html#4) For the mouse mm10 genome we load the package **BSgenome.Mmusculus.UCSC.mm10**. ```r library(BSgenome.Mmusculus.UCSC.mm10) BSgenome.Mmusculus.UCSC.mm10 ``` ``` ## Mouse genome: ## # organism: Mus musculus (Mouse) ## # genome: mm10 ## # provider: UCSC ## # release date: Sep 2017 ## # 239 sequences: ## # chr1 chr2 chr3 ## # chr4 chr5 chr6 ## # chr7 chr8 chr9 ## # chr10 chr11 chr12 ## # chr13 chr14 chr15 ## # ... ... ... ## # chrX_KZ289094_fix chrX_KZ289095_fix chrY_JH792832_fix ## # chrY_JH792833_fix chrY_JH792834_fix chr1_KK082441_alt ## # chr11_KZ289073_alt chr11_KZ289074_alt chr11_KZ289075_alt ## # chr11_KZ289077_alt chr11_KZ289078_alt chr11_KZ289079_alt ## # chr11_KZ289080_alt chr11_KZ289081_alt ## # (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator ## # to access a given sequence) ``` --- ## Creating a reference genome We will only use the major chromosomes for our analysis so we may exclude random and unplaced contigs. Here we cycle through the major chromosomes and create a [**DNAStringSet** object from the retrieved sequences](https://rockefelleruniversity.github.io/Bioconductor_Introduction/presentations/slides/SequencesInBioconductor.html#22). ```r mainChromosomes <- paste0("chr", c(1:19, "X", "Y", "M")) mainChrSeq <- lapply(mainChromosomes, function(x) BSgenome.Mmusculus.UCSC.mm10[[x]]) names(mainChrSeq) <- mainChromosomes mainChrSeqSet <- DNAStringSet(mainChrSeq) mainChrSeqSet ``` ``` ## DNAStringSet object of length 22: ## width seq names ## [1] 195471971 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chr1 ## [2] 182113224 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chr2 ## [3] 160039680 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chr3 ## [4] 156508116 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chr4 ## [5] 151834684 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chr5 ## ... ... ... ## [18] 90702639 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chr18 ## [19] 61431566 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chr19 ## [20] 171031299 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chrX ## [21] 91744698 NNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNN chrY ## [22] 16299 GTTAATGTAGCTTAATAACAA...TACGCAATAAACATTAACAA chrM ``` --- ## Creating a reference genome Now we have a **DNAStringSet** object we can use the [**writeXStringSet** to create our FASTA file of sequences to align to.](https://rockefelleruniversity.github.io/Bioconductor_Introduction/presentations/slides/SequencesInBioconductor.html#22) ```r writeXStringSet(mainChrSeqSet, "BSgenome.Mmusculus.UCSC.mm10.mainChrs.fa") ``` --- ## Creating an Rsubread index We will be aligning using the **subjunc** algorithm from the folks behind subread. We can therefore use the **Rsubread** package. Before we attempt to align our FASTQ files, we will need to first build an index from our reference genome using the **buildindex()** function. The [**buildindex()** function simply takes the parameters of our desired index name and the FASTA file to build index from.](https://rockefelleruniversity.github.io/Bioconductor_Introduction/presentations/slides/AlignmentInBioconductor.html#14) REMEMBER: Building an index is memory intensive and by default is set to 8GB. This may be too large for your laptop or desktop computer. ```r library(Rsubread) buildindex("mm10_mainchrs", "BSgenome.Mmusculus.UCSC.mm10.mainChrs.fa", memory = 8000, indexSplit = TRUE) ``` --- ## Rsubread RNAseq alignment We can align our raw sequence data in FASTQ format to the new FASTA file of our mm10 genome sequence using the **Rsubread** package. Specifically we will be using the **subjunc** function as it is splice aware. This means it will detect reads that span introns. This is the major difference between alignment of RNAseq and other genomic technologies like DNAseq and ChIPseq where we will use the align function. We can also provide a SAF or GTF to our Rsubread call. Although largely unnecessary for gene expression estimation, this will allow us to capture non-canonical splice sites. We simply need to provide a SAF/gtf to **annot.ext** parameter and set **useAnnotation** and **isGTF** to FALSE/TRUE depending on whether we use SAF or GTF as external data. --- ## SAF format using exons() SAF format is used by Rsubread to hold feature information. We simply need a table of exons' chromosome locations (chromosome,start,end,strand) and a feature/metafeature ID. We can retrieve exon locations and their gene ids using **exons()** function. We further select only exons which are annotated to exactly 1 gene. ```r library(TxDb.Mmusculus.UCSC.mm10.knownGene) myExons <- exons(TxDb.Mmusculus.UCSC.mm10.knownGene, columns = c("tx_id", "gene_id")) myExons <- myExons[lengths(myExons$gene_id) == 1] myExons ``` ``` ## GRanges object with 376333 ranges and 2 metadata columns: ## seqnames ranges strand | tx_id ## <Rle> <IRanges> <Rle> | <IntegerList> ## [1] chr1 4807788-4807982 + | 14 ## [2] chr1 4807823-4807982 + | 15 ## [3] chr1 4807830-4807982 + | 16 ## [4] chr1 4807892-4807982 + | 17 ## [5] chr1 4807896-4807982 + | 18 ## ... ... ... ... . ... ## [376329] chrUn_JH584304 55112-55701 - | 142445,142446 ## [376330] chrUn_JH584304 56986-57151 - | 142445,142446 ## [376331] chrUn_JH584304 58564-58835 - | 142445 ## [376332] chrUn_JH584304 58564-59690 - | 142446 ## [376333] chrUn_JH584304 59592-59667 - | 142445 ## gene_id ## <CharacterList> ## [1] 18777 ## [2] 18777 ## [3] 18777 ## [4] 18777 ## [5] 18777 ## ... ... ## [376329] 66776 ## [376330] 66776 ## [376331] 66776 ## [376332] 66776 ## [376333] 66776 ## ------- ## seqinfo: 66 sequences (1 circular) from mm10 genome ``` --- ## SAF format With the exons GRanges we can create the appropriate data.frame of SAF format for Rsubread. ```r dfExons <- as.data.frame(myExons) SAF <- data.frame(GeneID = dfExons$gene_id, Chr = dfExons$seqnames, Start = dfExons$start, End = dfExons$end, Strand = dfExons$strand) ``` --- ## RNA alignment with external annotation Now we have our SAF formatted exon information we can provide the SAF data.frame to the **annot.ext** argument, set **isGTF** as FALSE and set **useAnnotation** to TRUE. ```r myMapped <- subjunc("mm10_mainchrs", "ENCFF332KDA.fastq.gz", output_format = "BAM", output_file = "Treg_1.bam", useAnnotation = TRUE, annot.ext = SAF, isGTF = FALSE, nthreads = 4) ``` --- ## Sort and index reads As before, we sort and index our files using the [**Rsamtools** packages **sortBam()** and **indexBam()** functions respectively.](https://rockefelleruniversity.github.io/Bioconductor_Introduction/presentations/slides/AlignedDataInBioconductor.html#11) The resulting sorted and indexed BAM file is now ready for use in external programs such as IGV as well as for further downstream analysis in R. ```r library(Rsamtools) sortBam("Treg_1.bam", "Sorted_Treg_1") indexBam("Sorted_Treg_1.bam") ```

 --- class: inverse, center, middle # Counting with aligned RNAseq data

 --- ## Counting in gene models With our newly aligned reads it is now possible to assign reads to genes in order to quantify a genes' expression level (as reads) within a sample. First we need to gather our gene models of exons and splice junctions which we can use in our later counting steps. ```r library(TxDb.Mmusculus.UCSC.mm10.knownGene) geneExons <- exonsBy(TxDb.Mmusculus.UCSC.mm10.knownGene, by = "gene") class(geneExons) ``` ``` ## [1] "CompressedGRangesList" ## attr(,"package") ## [1] "GenomicRanges" ``` --- ## Counting in gene models Now we have our GRangesList with each entry corresponding to a gene and within each entry a GRanges object of the genes' exons. ```r geneExons[1:2] ``` ``` ## GRangesList object of length 2: ## $`100009600` ## GRanges object with 9 ranges and 2 metadata columns: ## seqnames ranges strand | exon_id exon_name ## <Rle> <IRanges> <Rle> | <integer> <character> ## [1] chr9 21062393-21062717 - | 233853 <NA> ## [2] chr9 21062400-21062717 - | 233855 <NA> ## [3] chr9 21062894-21062987 - | 233856 <NA> ## [4] chr9 21063314-21063396 - | 233857 <NA> ## [5] chr9 21066024-21066377 - | 233858 <NA> ## [6] chr9 21066940-21067093 - | 233859 <NA> ## [7] chr9 21066940-21067925 - | 233860 <NA> ## [8] chr9 21068030-21068117 - | 233867 <NA> ## [9] chr9 21073075-21073096 - | 233869 <NA> ## ------- ## seqinfo: 66 sequences (1 circular) from mm10 genome ## ## $`100009609` ## GRanges object with 8 ranges and 2 metadata columns: ## seqnames ranges strand | exon_id exon_name ## <Rle> <IRanges> <Rle> | <integer> <character> ## [1] chr7 84935565-84941088 - | 190288 <NA> ## [2] chr7 84943141-84943264 - | 190289 <NA> ## [3] chr7 84943504-84943722 - | 190290 <NA> ## [4] chr7 84943504-84947000 - | 190291 <NA> ## [5] chr7 84946200-84947000 - | 190292 <NA> ## [6] chr7 84947372-84947651 - | 190293 <NA> ## [7] chr7 84948507-84949184 - | 190294 <NA> ## [8] chr7 84963816-84964115 - | 190295 <NA> ## ------- ## seqinfo: 66 sequences (1 circular) from mm10 genome ``` --- ## Counting in gene models We can now use the **summarizeOverlaps()** to [count the reads in our BAM that overlap genes](https://rockefelleruniversity.github.io/Bioconductor_Introduction/presentations/slides/Summarising_Scores_In_Bioconductor.html#30). We specify a BamFile object using the **BamFile()** function and specifying the **yieldSize** parameter to 10000 to control memory footprint. The resulting **RangedSummarizedExperiment** object containing our counts and **GRanges** object. ```r library(GenomicAlignments) myBam <- BamFile("Sorted_Treg_1.bam", yieldSize = 10000) tregGeneCounts <- summarizeOverlaps(geneExons, myBam, ignore.strand = TRUE) tregGeneCounts ``` ``` ## class: RangedSummarizedExperiment ## dim: 24594 1 ## metadata(0): ## assays(1): counts ## rownames(24594): 100009600 100009609 ... 99929 99982 ## rowData names(0): ## colnames(1): Sorted_Treg_1.bam ## colData names(0): ``` --- ## Counting in exons models If want to start to evaluate differential transcript usage we will often evaluate counts over exons and assess for changes in exon usage.

 --- ## Counting in exons models To count over exons however we will encounter an issue of assigning reads to overlapping exons.

 --- ## Counting in exons models We can then work to differentiate exons by collapsing exons to the nonoverlapping, disjoint regions.

 --- ## Counting in exons models We can use the GenomicFeatures' package's **disjointExons()** function with our TxDb object, TxDb.Mmusculus.UCSC.mm10.knownGene, to extract a GRanges of our disjoint exons with their associated **gene_id**, **tx_name**, **exonic_part** in the metadata columns. We add some sensible names to our GRanges for use in later steps. ```r library(GenomicFeatures) nonOverlappingExons <- disjointExons(TxDb.Mmusculus.UCSC.mm10.knownGene) ``` ``` ## Warning: disjointExons() is deprecated. Please use exonicParts() instead. ``` ```r names(nonOverlappingExons) <- paste(mcols(nonOverlappingExons)$gene_id, mcols(nonOverlappingExons)$exonic_part, sep = "_") nonOverlappingExons[1:3, ] ``` ``` ## GRanges object with 3 ranges and 3 metadata columns: ## seqnames ranges strand | gene_id ## <Rle> <IRanges> <Rle> | <CharacterList> ## 100009600_1 chr9 21062393-21062399 - | 100009600 ## 100009600_2 chr9 21062400-21062717 - | 100009600 ## 100009600_3 chr9 21062894-21062987 - | 100009600 ## tx_name ## <CharacterList> ## 100009600_1 ENSMUST00000115494.2,ENSMUST00000216967.1 ## 100009600_2 ENSMUST00000115494.2,ENSMUST00000216967.1,ENSMUST00000213826.1 ## 100009600_3 ENSMUST00000115494.2,ENSMUST00000213826.1 ## exonic_part ## <integer> ## 100009600_1 1 ## 100009600_2 2 ## 100009600_3 3 ## ------- ## seqinfo: 66 sequences (1 circular) from mm10 genome ``` --- ## Counting in exons models We can now again use the **summarizeOverlaps()** function with our nonOverlapping, disjoint exons to identify a BAM file of interest. We need to set the **inter.feature** to FALSE to allow us to count reads overlapping multiple features (such as a read spanning between two exons). ```r tregExonCounts <- summarizeOverlaps(nonOverlappingExons, myBam, ignore.strand = TRUE, inter.feature = FALSE) ``` --- ## Counting in exons models Now we can review our counts from our gene-level and exon-level counting. We retrieve a matrix of counts from either **RangedSummarizedExperiment** object using the **assay()** function. ```r geneCounts <- assay(tregGeneCounts) exonCounts <- assay(tregExonCounts) head(exonCounts, 2) ``` ``` ## Sorted_Treg_1.bam ## 100009600_1 0 ## 100009600_2 1 ``` ```r head(geneCounts, 2) ``` ``` ## Sorted_Treg_1.bam ## 100009600 1 ## 100009609 0 ``` --- class: inverse, center, middle # Transcript quantification with pseudo-alignment

 --- ## Transcript quantification More recently methods have developed to directly quantify transcript abundance from FASTQ files using k-mer counting. k-mer counting offers a super fast method of gaining transcript abundance estimates, but does not produce a genomic alignment so not so useful for visualization. As we are most often interested in gene expression changes this offers a fast alternative to counting for alignment and counting. The two leading pieces of software for k-mer counting * [Salmon](http://salmon.readthedocs.io/en/latest/) - Relationship with DESeq2. * [Kallisto](https://pachterlab.github.io/kallisto/about) - History of splice aware aligners and transcript quantification. --- ## Salmon Salmon is the latest in a set of k-mer counting tools from the Kingsford lab (Jellyfish and Sailfish) and offers a workflow for transcript quantification from FASTQ raw sequencing data and a FASTA file of transcript sequences. ![](imgs/salmon.png) --- ## Installing programs that aren't in R There is no R package for Salmon. It is possible to install it on Mac and Linux using the [Anaconda](https://anaconda.org/bioconda/salmon) package repository (unfortunately there is not a Windows implementation). Anaconda is a huge collection of version controlled packages that can be installed through the conda package management system. With conda it is easy to create and manage environments that have a variety of different packages in them. Though there is no Salmon R package, we can interact with the anaconda package system using the R package [Herper](https://bioconductor.org/packages/release/bioc/html/Herper.html). This was created by us here at the BRC and is part of Bioconductor. ```r BiocManager::install("Herper") library(Herper) ``` --- ## Install Salmon with Herper First, we will use Herper to install Salmon with the *install_CondaTools* function. We just need to tell *install_CondaTools* what tool/s you want and the name of the environment you want to build. ```r salmon_paths <- install_CondaTools(tools = "salmon", env = "RNAseq_analysis") salmon_paths ``` Behind the scenes, Herper will install the most minimal version of conda (called miniconda), and then will create a new environment into which Salmon will be installed. When you run the function it prints out where Salmon is installed. There are additional arguments to control where miniconda is installed using *pathToMiniConda* and also update an existing environment with *updateEnv*. --- ## Reference for transcript quantification Once Salmon is installed we need to make a Salmon index. First we need a FASTA file of transcript sequences. We can use the GenomicFeatures' packages **extractTranscriptSeqs** function to retrieve a DNAstringSet object of transcript sequences using our sequence data from **BSgenome.Mmusculus.UCSC.mm10** and gene models from **TxDb.Mmusculus.UCSC.mm10.knownGene** object. ```r allTxSeq <- extractTranscriptSeqs(BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, use.names = TRUE) allTxSeq ``` --- ## Reference for transcript quantification With our new DNAstringSet object of transcript sequences we can write a FASTA file for use in Salmon with the **writeXStringSet** function. ```r writeXStringSet(allTxSeq, "mm10Trans.fa") ``` --- ## Reference with decoy sequences We can also provide a set of decoy sequences for building an index. This allows salmon to consider similar sequences outside of transcriptomic regions when mapping. To do this we need to add the main chromosomes to our transcriptome FASTA for creating an index. ```r mainChromosomes <- paste0("chr", c(1:19, "X", "Y", "M")) mainChrSeq <- lapply(mainChromosomes, function(x) BSgenome.Mmusculus.UCSC.mm10[[x]]) names(mainChrSeq) <- mainChromosomes mainChrSeqSet <- DNAStringSet(mainChrSeq) gentrome <- c(allTxSeq, mainChrSeqSet) ``` --- ## Reference with dummy sequence We will also need to provide a config file containing the names of sequences to be used for decoys. ```r writeXStringSet(gentrome, "mm10Gentrome.fa") write.table(as.data.frame(mainChromosomes), "decoy.txt", row.names = FALSE, col.names = FALSE, quote = FALSE) ``` --- ## Salmon index from R As with standard aligners, the first part of our quantification requires us to make an index from our FASTA file using the **Salmon index** command. We specify the transcript FASTA file (-t) and index name (-i). Here we arrange our Salmon command into a system call from R. This means we are directly triggering an OS command from within R. ```{} salmon index -i mm10Trans -t mm10Trans.fa ``` Herper allows us to run conda packages from within R. Salmon has been installed into the environment *RNAseq_analysis*. So we can use this environment from R using *with_CondaEnv()*. ```r fastaTx <- "mm10Trans.fa" indexName <- "mm10Trans" with_CondaEnv("RNAseq_analysis", system2(command="salmon",args = c("index", "-i",indexName, "-t",fastaTx), stdout = TRUE)) ``` --- ## Salmon index from R To create index with decoys we provide our transcriptome + chromosome FASTA as well as our decoy file to the -d paramter. ```r with_CondaEnv("RNAseq_analysis", system2(command="salmon",args = c("index", "-i",indexName, "-t",fastaTx, "-d decoy.txt"), stdout = TRUE)) ``` --- ## Salmon quant from R To quantify transcript abundance we use the **Salmon quant** command. We specify the index location (-i), the reads to quantify (-r), the output directory (-o) and the library type as automatic detection of type (-l A). ```{} salmon quant -i mm10Trans -r ~/Downloads/ENCFF332KDA.fastq.gz -o TReg_1_Quant -l A ``` ```r fq <- "ENCFF332KDA.fastq.gz" outDir <- "TReg_1_Quant" with_CondaEnv("RNAseq_analysis", system2(command="salmon",args = c("quant", "-i",indexName, "-o",outDir, "-l A", "-r",fq), stdout = TRUE)) ``` --- ## Salmon outputs The output from Salmon is our quantification of transcripts in the **quant.sf** file in the user defined output directory. We will use a new package **tximport** to handle these counts in next session, but for now we can review file using standard data import R libraries. ```r myQuant <- read.delim("TReg_1_Quant/quant.sf") myQuant[1:3, ] ``` ``` ## Name Length EffectiveLength TPM NumReads ## 1 ENSMUST00000193812.1 1070 820.000 0.0000 0 ## 2 ENSMUST00000082908.1 110 3.749 0.0000 0 ## 3 ENSMUST00000192857.1 480 230.000 0.8368 7 ``` --- ## Time for an exercise [Link_to_exercises](../../exercises/exercises/RNAseq_part1_exercise.html) [Link_to_answers](../../exercises/answers/RNAseq_part1_answers.html)


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LEARN MORECrafty Crafts offers a large variety of produce, eggs, canned goods and handcrafted items at the market year round.
LEARN MORENature has a way of guiding us all, and a piece of it in your home is special. Every tree has unique character that is rare and beautiful.
LEARN MOREStuarto's Olive Oil Company specializes in imported extra virgin olive oils, balsamic vinegars, and specialty oils from award-winning artisan and small-run producers around the world.
LEARN MOREWe offer fresh homemade breads: sourdough, rye, wheat & cinnamon raisin. We also have assorted brownies cakes & pies, take & bake entrees, and cooked breakfast on site!
LEARN MOREWe are a family owned flower farm specializing in heirloom and unique flower varieties. We use organic and sustainable practices to bring you beautiful flowers and custom arrangements.
LEARN MORETom and Lori have been handcrafting the highest quality wood crafted products for over 40 years. From small to large, they are well equipt to produce products you will fall in love with.
LEARN MORE


Connect Chess
Linking the world wide webchess
Sometime ago (this sentence is getting old one day per day) I thought of new abstract
game, called Gonnect, where you apply the GO rules in order to connect two opposite sides
of the 19x19 go board. Almost instantly I take that idea and reuse it on chess.
Connect Chess
- All Chess rules apply except in the following:
- Definition: A Link between 2 pieces (at least one must not be a pawn)
occur when one of them could move to the other's square (if it was empty) and they do not
share the same rank.
- A player wins if he can create a link between a set of his pieces from the 1st to the
last rank of the board.
note: A player cannot create a link with two consecutive pawns, they are just
used has nodes between two non pawn pieces.
 n .  p .  N . .
 O O O
R N B . Q R K . is a win for White (Link Qe1->e5<-Bb8). (
back to top


Suraj Shaw
Switch SOCIETY ERP
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Clients & Works
You might note that some of these sites cant be loaded, sorry.. they are more than 2 years old, and their owners might have brought them down
Compiling...
You might note that some of these sites cant be loaded, sorry.. they are more than 2 years old, and their owners might have brought them down


Next: SLA_S2TP - Spherical to Tangent Plane
Up: SUBPROGRAM SPECIFICATIONS
Previous: SLA_RVLSRD - RV Corrn to Dynamical LSR
- ACTION:
- Velocity component in a given direction due to the Sun's
motion with respect to a kinematical Local Standard of Rest.
- CALL:
- R = sla_RVLSRK (R2000, D2000)
- GIVEN:
-
| R2000,D2000 |
R |
J2000.0 mean (radians) |
- RETURNED:
-
| sla_RVLSRK |
R |
Component of standard solar motion
in direction R2000,D2000 (km s-1) |
- NOTES:
- 1.
- Sign convention: the result is positive when
the Sun is receding from the given point on the sky.
- 2.
- The Local Standard of Rest used here is one of several
kinematical LSRs in common use. A kinematical LSR is the
mean standard of rest of specified star catalogues or stellar
populations. The Sun's motion with respect to a kinematical
LSR is known as the standard solar motion.
- 3.
- There is another sort of LSR, seldom used by observational
astronomers, called the dynamical LSR. This is a
point in the vicinity of the Sun which is in a circular orbit
around the Galactic centre. The Sun's motion with respect to
the dynamical LSR is called the peculiar solar motion. To
obtain a radial velocity correction with respect to the
dynamical LSR use the routine sla_RVLSRD.
- 4.
- The adopted standard solar motion is 20 km s-1
towards (1900).
- REFERENCES:
- 1.
- Delhaye (1965), in Stars and Stellar Systems, vol 5, p73.
- 2.
- Methods of Experimental Physics (ed Meeks), vol 12,
part C, sec <IP_ADDRESS>, p281.
Next: SLA_S2TP - Spherical to Tangent Plane
Up: SUBPROGRAM SPECIFICATIONS
Previous: SLA_RVLSRD - RV Corrn to Dynamical LSR
SLALIB --- Positional Astronomy Library
Starlink User Note 67
P. T. Wallace
12 October 1999
E-mail:ptw@star.rl.ac.uk


{% extends "global/Page.html" %} {% load otree static %} {% block title %} Employees' Bonus Distribution {% if pay_transparent == 1 %} (Pay Transparent Condition) {% else %} (Pay Secret Condition){% endif %} {% endblock %} {% block content %}
The employee bonus pool will be distributed among the three employees by the Manager. Specifically, the Manager will allocate the bonus pool by entering the bonus amounts, in points, in the computer. The sum of the three bonuses must equal the total employee bonus and no employee can receive less than zero.
{% if pay_transparent == 1 %}All three employees will be informed of:
The employees will learn, in private, about their own bonus amount. The employees will NOT be informed of:


VCBoss
Present UIViewControllers modally in an easy and safe way. No more Fatal Exception: NSInvalidArgumentException Application tried to present modally an active controller ...
errors. Easily present, dismiss, replace, and swap UIViewControllers presented modally in a presenting UIViewController.
Why?
In my iOS apps, I enjoy presenting, dismissing, replacing, swapping in and out UIViewControllers modally. It’s a nice way to present subviews in a main UI for a user to interact with.
However, managing all of those presented UIViewControllers is risky business. What if I am already showing a user a UIViewController and I want to display another one after that? What if I want to replace the currently shown UIViewController with a new one after the user presses an Accept
button? There are many use cases that VCBoss can be used for. Managing all of these use cases manually in a presenting UIViewController becomes a pain very quickly.
Features
VCBoss comes with the basic functionality you’re already used to:
- Present a UIViewController modally.
- Dismiss a UIViewController that was presented modally.
Pretty simple, right? However, here is where VCBoss makes me happy 😄:
- Present a UIViewController modally immediately (if the presenting UIViewController is not presenting a UIViewController already) or add to the end of the stack to be presented in the future.
- Present a UIViewController forcefully by dismissing a currently shown UIViewController if there is one and then show the new UIViewController. Do not worry, the UIViewController that gets dismissed, if there is one, will be presented after the forced UIViewController gets dismissed. It’s like someone cuts to the front of the line.
- Replace the currently shown UIViewController, if there is one, with a new UIViewController.
- Dismiss a UIViewController and have the next one in line automatically shown next.
- Dismiss all UIViewControllers currently in the stack of UIViewControllers shown and to be shown.
All of these operations are performed with 1 line of code without running the risk of getting, Fatal Exception: NSInvalidArgumentException Application tried to present modally an active controller ...
thrown by trying to present 2+ UIViewControllers at once.
How?
VCBoss uses a very familiar API.
- To present a new UIViewController modally immediately (if the presenting UIViewController is not presenting a UIViewController already) or add to the end of the stack to be presented in the future after previous UIViewControllers are dismissed by VCBoss:
self.vcboss.present(newViewController, animated: true, completion: nil)
- To dismiss a UIViewController:
presentedViewController.vcboss.dismiss(animated: true, completion: nil)
or
presentingViewController.vcboss.dismiss(presentedViewController, animated: true, completion: nil)
These are the 2 functions you are already used to using in your code. To start using VCBoss, all you need to do is replace all of your instances of self.present()
with self.vcboss.present()
and all instances of viewController.dismiss()
with viweController.vcboss.dismiss()
. Just add the extension and you’re done.
To make life easier, check out the section on how to determine where you’re using self.present()
and
viewController.dismiss()` already in your app to replace with VCBoss.
Below are added functionality that UIKit does not give you that VCBoss does.
- To replace the currently shown UIViewController with a new UIViewController:
self.vcboss.replace(with: newViewController, animated: true, completion: nil)
- Present a new UIViewController immediately, dismissing a UIViewController if there is one already shown and bring it back after this new UIViewController gets dismissed:
self.vcboss.present(newViewController, animated: true, completion: nil, force: true)
- Present a new UIViewController only if there is not one already presented:
self.vcboss.presentOnlyIfNothingAlreadyShown(newViewController, animated: true, completion: nil)
- Dismiss the currently shown UIViewController and do not show anymore that may have been added before. Clear the stack to start over.
self.vcboss.dismissAll(animated: true, completion: nil)
- If you need to get the number of UIViewControllers currently presented + UIViewControllers in stack to be shown in future after currently presented UIViewController gets dismissed:
self.vcboss.numViewControllersPresenting
Docs
Check out the docs here. If something is confusing, please, open an issue.
Example
To run the example iOS app:
- Clone the repo.
- Run
pod install
from theExample/
directory. - Run app from XCode by opening
VCBoss
workspace.
Installation
VCBoss is available through CocoaPods. To install it, simply add the following line to your Podfile:
pod 'VCBoss'
Note: I recommend appending the version of the cocoapod to the Podfile line entry like: pod "VCBoss", '~> 0.1.0'
because this library at this time does not provide the guarantee of backwards compatibility. Be aware when using it the API can change at anytime. I don’t want your code to break the next time you call pod update
:).
The latest version at this time is:
SwiftLint
VCBoss does not work well (it tries it’s best, but cannot guarantee anything) if you use self.present()
and self.dismiss()
to present/dismiss UIViewControllers. You must use the VCBoss class to do all of the presenting and dismissing.
But, we are all human. It’s easy to use your habits and use self.present()
in your app. To help, I recommend you use SwiftLint to throw errors whenever you use either of these two methods. When you try and compile your code, SwiftLint will throw an XCode error not allowing you to continue until you fix your code.
To use SwiftLint, all you need to do is:
- Install SwiftLint into your iOS project (super easy. I use this method).
- Add the following to your
.swiftlint.yml
file:
custom_rules:
use_vcboss_present:
included: ".*\\.swift"
excluded: ".*Test\\.swift"
regex: "(self\.present\()"
message: "Use self.vcboss.present() instead."
severity: error
use_vcboss_dismiss:
included: ".*\\.swift"
excluded: ".*Test\\.swift"
regex: "(self\.dismiss\()"
message: "Use self.vcboss.dismiss() instead."
severity: error
Author
- Levi Bostian - GitHub, Twitter, Website/blog
Development
Documentation
The docs are generated and hosted by cocoapods automatically for cocoadocs.
The docs are generated via jazzy using command: jazzy --podspec VCBoss.podspec
(assuming jazzy is installed. If not: gem install jazzy
)
License
VCBoss is available under the MIT license. See the LICENSE file for more info.
Credits
Header image: Photo by rawpixel.com on Unsplash
Inspiration for some of the API from Kingfisher. I tried to make the library easy to use and as backwards compatible as possible with existing UIKit code, Kingfisher’s API seemed like a great with with it’s use of extensions and easy to use code.


Nyzo version 597 (commit on GitHub) adds BlockManager initialization to the CycleTransactionSignScript.
This version only affects CycleTransactionSignScript.
In version 588, initialization of BlockManager was changed from a static block in the class to a requirement that the BlockManager.initialize() method be called manually. The release notes stated:
Also, the static block has been removed. This is a significant, far-reaching change. This change has been fully tested for the verifier, sentinel, and client, but it may still have some unintended effects on scripts. This will continue to be reviewed.
One of the affected scripts is the CycleTransactionSignScript. In this script, BlockManager is now explicitly initialized.


There is no deadline to register, you may register to vote up to and including the day of the election. However,if you register online the day before the election or on Election Day, your application may not be processed and your name may not appear on the checklist and you may be asked to fill out another application at the polls. To be sure your name appears on the checklist, please register by the Friday before the election.
Get Started:
1. Fill in all of the required fields on this application.
2. You are not registered to vote until your application is approved by the Town Clerk.
3. You should receive an acknowledgment within two to four weeks after submitting or mailing your registration. Please contact
your Town Clerk if you have not received any information within this time.
4. If you are registering to vote in Vermont for the first time, you must include a photocopy of an acceptable form of ID. Acceptable forms of ID are: ● Valid photo ID (driver’s license or passport) ● Current utility bill ● Current bank statement ● Another government document containing your residential address.
You may use this system to:
(1) register to vote in Vermont, (2) change your name and/or address on your current voter registration record.
WARNING: A person who makes false statements on this application shall be subject to federal or state criminal penalties of up to a $10,000 fine, or imprisonment for not more than 15 years, or both. (17 V.S.A. § 2145(f); 17 V.S.A. § 2011; 42 U.S.C. § 1973gg-10).


{% extends "layout_unbranded.html" %} {% block page_title %} Money Claims Prototype {% endblock %} {% block home_link %} index {% endblock %} {% block content %} Account created You can now sign in to your account. Continue {% include 'prototypes/prototype-mar-2019/includes/contact.html' %} {% endblock %}
You can now sign in to your account.


Provides plugins, classes and interfaces for working with Helm, by way of the microbean-helm project, from Maven.


{% extends "global/Page.html" %} {% load otree static %} {% block title %} Interaction Rules - Swap {% endblock %} {% block content %}
In the following rounds, you will exchange positions under Swap:
When you finish reading, please press next to take a quiz before you start the game. You can always review the instruction by clicking the "Review the Instruction" button at the end of the pages when you are at quiz pages and result pages.
{% next_button %} {% endblock %}


Hi, I am a Passionate, profoundly enthusiastic Web Developer. I Have powerful desire for knowledge and challenges. Actively involved with the latest technology and recent innovation in the web developing field. I am a Self-educated, self-motivated and flexible person. Also fast learner who picks up new skills rapidly and enthusiastic in breaking new grounds.
I am self-educated designer and language specialist. Highly Intresed in hunting down new skills and have years of experience in Graphic designing as a freelance and teaching. Currently I am a fullstack Web Developer with well experience in Python Django. I love to design amazing front-end using html, css, javascript and bootstrap. I love spending time on fixing little details and optimizing web apps. Also I like working in a team, I can share my experience and we can learn faster and much more. As the saying goes: 'two heads are better than one'


Software Developer looking for out of the box opportunities.
I am currently a Computer Science Graduate Student at Indiana University with proficiency in Linux Management tools/softwares, web services and applied machine learning techniques.
Click here for my complete resume.
I am currently the TA Lead for Inforamation Infrastructure and Python courses.My responsibilities include designing course structure, conducting labs, grading assignments and clarifying student's doubts.
Currently working with Prof. Feng Quain on head mounted displays for 360 degree video streaming.My responsibilities include developing machine learning models for predicting head movements,conducting user study to collect traces of user activities while watching a VR video and utilizing these traces to train the models.
I worked on a data sanitisation tool where I developed a cloud based data optimization utility tool that discovers and deletes data that is no longer in use. I implemented RESTful services using multi-node MVC architecture approach with GraphQL endpoint.I also developed the client side module that secure deletes data on any operating system when requested by user and reports the status to the API server.
I worked for a Canada based client where my major job responsibilities included developing and executing test scripts for functional testing.I also worked in automation testing using selenium and java. My other responsibilities included automating monthly budget tracker, developing reports on forecasting, communicating with the onshore clients to fulfill business requirements and develop business models.
I worked in the Information Systems Department where my team was responsible for developing a tool that analyze lube fuel ratio, sales growth and average sales of lubes and generate performance metric reports for business stakeholders.I designed and implemented jsp pages to fetch data. I also worked on optimizing and tuning SQL Queries to improve performance and response time.
This software recognizes real time facial expressions which are universally expressed and recognized across all cultures.Developed a deep Convolutional network architecture that extracts facial features of the user from a live video application and instantly returns their emotion.
Developed a model that predicts stock market trends from twitter feeds. Our LSTM+CNN and SVM models uses human sentiment to predict stock behaviors for a any set of companies.
Worried about your mobile's battery usage? We've got you covered! This project gives a comparative analysis of energy usage and data consumption of a mobile application client and a web browser client for the same service and suggest methods to optimize mobile app performance.We have used AT&T's ARO tool for our study.Our study was performed over Facebook, Youtube and Amazon.
This is an image stitching tool that lets you create your own panoramic image.This tool performs feature matching ,warping and blending over multiple overlapping images and produces a sweeping landscape!
Built XGBoost Logistic Regression and Random Forest models to predict whether a driver will initiate an auto insurance claim for the next year.
This is an UI-based easy to use tool that fetches real time monitoring results of instances and their network activities from any open-source cloud computing platform.Currently our tool works over Openstack.
Developed an AI gaming platform where ML Bots enter in a creative programming challenge.Participants design bots to compete in a specially designed arcade and board games. The Platform supports C/C++/Python/Java bots.
This is a web-based application designed for tour operators.This software manages cruise information for various destinations,their respective schedules and also allows tourists to make reservations accordingly.
I have been an active member of Women in Computing at IEEE Student Branch since past 4 years.
I listen to all kinds of music!Dolphin is my spirit animal.
Big Harry Potter fan!
Love travelling and aspire to be a nature photographer.


CMS Donation Summary
Ref #
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Amount
Date
Credit Card #
Actions
1
Shikha Naik
April, 14, 2015 10:10am
$45.00
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Shikha Naik
April, 14, 2015 10:10am
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Upon completing this lesson, you should be able to:
- Describe the relationship of organisms to human host
- Explain the difference between pathogen and opportunistic pathogen
- List the steps of an infection
- Describe the events of each stage of an infection
- Explain the differences between endotoxins and exotoxins
- Describe the concept of a reservoir
- List the purposes of epidemiology
- Define the basic terminology used by epidemiologists
- Explain the aspects of descriptive epidemiology
- Explain the meaning of epidemiological rates


Advisor Dr. Kathy Platoni
A nationally renowned expert in the treatment of PTSD for our veterans who has served for more than 3 decades as a clinical psychologist and served as a U.S Army Officer, retiring as a full Colonel after 4 wartime deployments. Dr. Platoni has developed combat stress control, debriefing, and crisis management programs used throughout the U.S. Army.
CEO Benjamin Greiner
Greiner is the CEO and founder of the non-profit organization The Mental Health Communication Project Co., a company that is changing the way we communicate about mental health. With the companies first website, Greiner led TalkAboutDepression to become a finalist for the 2018 Stu Lieblein ‘90 Pitch Contest.
For any inquires on how your organization can provide support contact
bengreiner@talkaboutdepression.org


The Emvents application will have two types of users or personas: attendees (people signing up to events) and organizers (people organizing events). We will differentiate the two different roles and implement some authorization rules.
Familiarize with ACL (Access Control Lists) for authorization, how to use the Node ACL Node library and how to configure Mongodb as database and use the Express.js middleware.
https://github.com/optimalbits/node_acl
Only the user who has created the event should be able to update or delete an event.
You should implement an endpoint that returns all the events organized (created) by a given user.
You should implement an endpoint that allows a user to sign up to (RSVP) an event.
You should implement an endpoint that returns all the upcoming events a user has signed up for.
You should implement an endpoint that allows the organizer of an event to see all the users who signed up to a given event he is organizing.
You should implement an endpoint that allows the organizer of an event to see all the users who signed up to a given event he is organizing.


We love lion
The lion (Panthera leo) is a large
cat of the genus Panthera native to Africa and India.
It has a muscular, deep-chested body, short, rounded head, round ears, and a hairy tuft at the end of its tail.
It is sexually dimorphic; adult male lions are larger than females and have a prominent mane. It is a social species,
forming groups called prides. A lion's pride consists of a few adult males, related females, and cubs.
Groups of female lions usually hunt together, preying mostly on large ungulates. The lion is an apex and keystone predator;
although some lions scavenge when opportunities occur and have been known to hunt humans, the species typically does not.


{% load static %}
{% include 'bases/head_base.html' %}
Settings
{% include 'bases/navbar_base.html' %}
{% if successful_changes|length > 0 %}
Your
{% for change in successful_changes %}
{{ change }}
{% if forloop.counter < successful_changes|length|add:"-1" %},
{% elif forloop.counter == successful_changes|length|add:"-1" %}
and
{% endif %}
{% endfor %}
{% if successful_changes|length == 1 %}
has
{% else %}
have
{% endif %}
been updated successfully.
{% if errors %}
Form errors have been marked in red.
{% endif %}
{% endif %}
{% include 'bases/modal_base.html' %}
{% include 'bases/footer_base.html' %}


Toggle navigation
World of Rations
Formulates on a true “Least-Cost” procedure
Indicates the composition and nutrient status
An all-species website – Alpaca to Zebra
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Selly Oak is the preferred neighbourhood for University of Birmingham Undergraduates
Do you like to live in a residential location well-connected to the city centre and enjoy a number of independent retailers? Do you like lindy hop and buddhist meditations? Then Moseley is the place for you!
Do you want to live in a leafy residential area close to the University of Birmingham and just about one mile to the city centre? Then Edgbaston is the place for you!
Do you want to live in a calm and residential area only two train stops away from Aston University? Erdington will be perfect for you!
If you want to live in a residential village with independent shops and restaurants, then Harborne is the place for you!
If you are a city person who cannot live far from one of the world's best concert hall and the best Birmingham shopping mall, consider living in Birmingham city centre!
Do you like to enjoy the peace of the canals and the buzz of Birmingham nightlife? If so, Brindleyplace is a fantastic location for you!


Blog Posts
41 posts, page 5 of 9
-
Routeless Backbone Contacts 2.0
Oct 3, 2011This post describes a revamped version 2.0 of my original Routeless Backbone Contacts application. The material covered here builds on the original post.
- The basic application functionality and the underlying data remains the same.
- The new user interface is a single two-pane page with a selectable list of contacts on the left and contact details on the right.
- A Search box has been added to incrementally filter the list of displayed contacts.
- The application is 100% event driven – there is no direct coupling between the views. Backbone.js events emitted by the underlying contact data collection ensure the views are updated automatically when the state of the underlying data changes.
-
Routeless Backbone Contacts
Sep 23, 2011You don’t need a URL router to write client-side applications.
Routeless Backbone.js Contacts is a totally client-side CRUD tutorial application written using CoffeeScript, Stylus, Backbone.js and jQuery which are a perfect match for writing concise, readable well structured web applications.
- The source is on Github.
Note: This release described in this post is at the 1.0 tag.
- Uses DOM events exclusively for UI navigation.
- The contacts data is persisted locally using browser Web Storage.
- Templates are written using Underscore.js templates (included with Backbone.js).
Note: A second version of this tutorial application [has been posted], it builds on the material covered in this post.
-
Switching from the iPad to the Asus Transformer
Aug 31, 2011My blogs are usually technical in content and try to be objective in character, this blog is a bit different, it has an unashamed subjective bias (you’ve been warned).
Shortly after the iPad 2 was released I went over to the Dark Side and brought one (my first and only Apple computer). I was just fed up waiting for a decent Android tablet. At the time my only requirements were a decent ePub reader and a web browser.
-
Fossil Backend for AsciiDoc
Aug 30, 2011The AsciiDoc Fossil backend plugin is hosted on Github, it generates Fossil friendly Wiki markup from AsciiDoc source. As of version 1.0.0 (2012-08-30) the Fossil backend plugin embeds linked images and admonition icons in the wiki documents.
-
Keeping a lid on Mobile data
Jul 17, 2011How to configure your Android phone to automatically turn off the mobile data connection once your mobile data limit is reached.


[Erowid Warning: Our understanding of the literature is that there is no such thing as safe use of volatile solvents, aerosols and other street inhalants : their psychoactive effects are inseparable from nerve and organ damage. We have chosen to include these reports to help document the real world use of inhalants, but their inclusion is not intended to imply that they are anything but dangerous.]
A very long time ago, I told myself that I'd never do any drug besides weed. Weed made me happy, weed was relatively easily obtainable, and I thought I'd never have the need for anything more than that. I was wrong. I am now in my second semester of college, and am just starting my 'experimental' phase. And the current thing I'm experimenting with is inhalants. Yeah, I know this is bad, and especially after the inhalant of which this report is concerned with, I fully plan to stop as soon as I can. Because I have a feeling that it's probably pretty bad for my body/brain. But man, these things are fun!
Anyway, I've tried nitrous whippits (my fav) and a couple other things, but I just read earlier today that the canned air computer dusters can be used to get fucked up. (I will warn you that as nitrous is my fav and probably the most popular, I will be comparing the effects of the duster to those of nitrous just because that is the only thing that even comes close to it.) So I trotted out to my local Circuit City and obtained a can of Interact brand 'Air Blaster'. It was about $8 including tax. If it matters, the chemical components section of the label says: '1,1,1,2-Tetrafluorethane' with a CAS of '811-97-2' (whatever that means).
Today's search for inhalants was started because my entire CD book thingy was stolen sometime last night, about 40-50 CDs that I've collected over several years. Needless to say, I was pretty pissed, and wanted something to raise my spirits. Being out of nitrous and low on funds, I decided to try the duster thing. So I went out and purchased it and came directly home. Not wanting to freeze my lungs as had been mentioned in a couple other reports, I just used my trusty nitrous balloon to inhale from - I filled it with about the same amount of duster stuff as normally comes out of a whippit, so I could see the difference in effects from roughly the same dosage of each. Using the same method as I use nitrous (exhale completely, then inhale the balloon slowly, and hold my breath as long as possible) I huffed the duster from the balloon. And the results were absolutely breathtaking!
As I was breathing it in, I noticed a very faint burning sensation in my throat, and it tasted fainly like the way rubbing alcohol smells. Then the effects started hitting me. They came on faster and harder than nitrous ever had. Everything in my field of vision started getting bright flashy spots all over it. Everything looked like I was looking at it on a TV with the contrast turned way up (light things were way lighter, dark things were way darker). The music I was listening to seemed to come from a very long ways away, even though the speakers are right behind my head. Every sound and movement was kind of echoey and vibratey, just like nitrous, but it was so much more intense! In one person's nitrous report they compared this effect to helecopters - yeah, that is a pretty accurate portrayal, but it sounded like I had an entire army of helecopters coming from inside my head.
Then everything started spinning and flying, as if I was underwater doing an infinite number of backflips. And that is the last definite separate effect that I remember. It was just a combination of the flashy lights and echoes/vibrations and flying/falling forwards and all sounds coming from a million miles away. And it stayed like that for at least two to three minutes, much much longer than nitrous.
Finally I started to come down, with all the effects gradually subsiding. I did two more balloons of the same amount after that (total 3 balloons, within about 15 minutes). It is now about an hour after I did the last one. Things still feel kinda 'not right' occasionally, but it's nothing to really be worried about (I hope). My eyes feel dry, and like there's more pressure than normal behind them. Only a very minor headache that seems to be decreasing as I write this, and my throat/lungs feel surprisingly normal considering how the stuff tasted and felt going down.
I have no plans to do anymore today, though I will probably eventually finish off the can either with myself or with a friend. And after that, I'm going to try very hard not to get anymore and just go back to nitrous, since I'm sure this stuff is pretty evil in the long run.
Experience Reports are the writings and opinions of the individual authors who submit them.
Some of the activities described are dangerous and/or illegal and none are recommended by Erowid.


By Christopher Watkins
March 10, 2016
***Breaking News: AlphaGo has won the first two matches!*** In this, the third in our series on the epic Go matches being played between AlphaGo (Google’s Artificial Intelligence software) and Lee Se-Dol (Current Go World Champion), we look at the history of Humans vs. Machines, and the innovations that have led us to this incredible moment in time.
For as long as humans have built things, we’ve wrestled with the implications of what we’ve built. In many cases, these philosophical and ethical wrestlings have made for great drama—think Frankenstein, or 2001: A Space Odyssey. Often, the hypothetical scenarios we envision come remarkably close to true, and the discoveries we’ve made in the fields of Artificial Intelligence and Machine Learning make clear that a “computer with a mind of its own” is going to take over the world not such a fantastic thing to imagine any longer.
Perhaps this is why we are so captivated by human vs. machine competitions, because the idea of being overcome by that which we’ve created speaks to something very deep within our collective consciousness. When IBM’s Deep Blue faced off against Garry Kasparov1, the event resulted in more than three billion impressions around the world, and when IBM’s later creation Watson challenged the champions on Jeopardy, millions of viewers were glued to the proceedings.
Taking place right now, there is an event that, while not likely to scale the same media heights, may in fact have far greater implications when it comes to the future of “intelligent” machines. On March 9, in Seoul, South Korea, a computing system know as AlphoGo (built by researchers at DeepMind—a Google Artificial Intelligence lab) began a five-game match against Lee Se-dol, one of the very best players in the world at the ancient game of Go.
Why is this so significant?
Here is how the DeepMind team explained it in their paper Mastering the Game of Go with Deep Neural Networks and Tree Search:
The game of Go has long been viewed as the most challenging of classic games for artificial intelligence due to its enormous search space and the difficulty of evaluating board positions and moves.
Put another way, winning at Go is a kind of Holy Grail for those who strive to create machines that can “think” on their own, because success at this uniquely complex game seems to require something more than just skill, knowledge, and experience. It requires intuition. Feel. Style. Characteristics we associate with humans, not with machines.


I recently graduated with a Bachelor of Cognitive Science degree specialized in Human-Computer Interaction from the University of California, San Diego. My interest in the brain and human behavior introduced me to study cognitive science at UCSD. I believe the user experience is the study of complex human behavior in response to a relationship with technology. As a user experience designer, I love applying ideas from my head into the real world, and I have a strong passion in design that is not only visually appealing but also user-friendly because the ultimate goal of the design is at people.
My goal, not only as a designer, but also as an individual, is to learn and to get inspired from different fields, cultures, and people. I am looking forward to more opportunities to gain valuable experiences.
I am originally from South Korea and currently live in sunny San Diego. When I am not working on my designs, I like to spend my time on reading novels, traveling the world, doodling, and watching movies.
I want to be someone who brings joys and positive influence on people around me.
Making my ideas into reality is one of the reasons why I love design.
I am hoping to face valuable challenges to be a better person.


4 references to Delete
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HTML5 Games
Shady Puzzle
Break It
Shady Puzzle
Arrange Numbers
Snake
Coming Soon...
Release Date: 12-May-2013


EFCC arrests five ‘Yahoo Yahoo Boys’ in Abia
by The Eagle OnlineOperatives of the Economic and Financial Crimes Commission Port Harcourt Zonal Office have arrested five suspected internet fraudsters at Exrico Lodge, behind Michael Okpara University of Agriculture, Umudike, Abia State.
They were arrested on Wednesday in a sting operation.
The suspects are: Onuoha Goodness Chinedu, Harry Victor, Basil Obidiegwu Chukwunaeke, Amayhayi Chukwuli and Nwabueze Nnaemeka.
Their arrest followed series of intelligence linking them with alleged fraudulent activities ranging from love scam on numerous dating sites to obtaining money by false pretences and other fraud still being investigated.
Items recovered from them at the point of arrest were an Apple laptop; seven mobile phones of various brands, two Wi-Fi devices and two power banks.
The suspects would soon be charged to court, a statement by the EFCC on Thursday said.


DISCLAIMER!! This is for demo purposes ONLY. This violates Youtube's Content Sharing Policy.
Video (.mp4)
Audio (.mp3)


This is the style guide that I follow when programming in Objective-C, this is for my own reference, but other people may find this useful.
General
- Use modern objective-c 2.0 syntax
- Use ARC whenever possible.
- Manual memory management should only be used when using older libraries that haven’t been updated yet.
- Use tabs when indenting, not spaces.
Code Naming Basics
- Follow the Apple naming guidelines
- Use descriptive names, even if they are long. Xcode has great code completion features. Use them.
- Clarity is preferred over all else.
- E.g. Compare the two methods:
[spaceship fly: 10.0f]
and[spaceship flyAtSpeed: 10.0f]
. - Note how much clearer the second declaration is, the method describes its intentions and parameter names.
- Don’t use abbreviations. E.g.
bgColor
vs.backgroundColor
- Custom resuseable classes should be prefixed with
AFG
- Application level classes do not have to be prefixed. E.g. ViewControllers
- All view controllers should be descriptively named and end with
ViewController
.- E.g.
CalculatorSettingsViewController
- E.g.
Commenting
- Follow the appledoc code formatting style.
- Only comment the method declarations. E.g. In the
@interface
or private@interface ... ()
code blocks. - Describe what the method does, the parameter names and the return value and what it signifies.
The following is a good example of method commenting:
/** This method asks the delegate if the AFGContainerViewController should pop the current view from the view stack.
@param - The current AFGContainerViewController object
@return A BOOL value indicating if the current view controller should be removed from the AFGContainerViewController's view stack.
*/
-(BOOL) AFGContainerViewControllerShouldPopContainerViewController: (AFGContainerViewController*) containerViewController;
Spacing
-(void) performOperationWithObject: (NSObject*) objectName {
NSLog(@"This is a well spaced method");
[objectName performSomeOperation];
}
- No space between the class or instance specifier
(+,-)
- Single space between the return type and method name
- Single spaces between method signature, object types and object names
- Brace on the same line as the method signature.
- Optional newline below the method signature for readability
- No newline before the closing brace
Variables and Initializers
- Variable names should always start with lower case.
- Good:
numberOfObjects
- Bad:
NumberOfObjects
- Good:
- Clearly identify the designated initializer for the class
- All other initializers should propagate up to and use the designated initializer.
- Override the superclass’ designated initializer.
- Initialization method should be at the top of the
@implementation
- Don’t explicitly initialize variables to nil. Under ARC this happens automatically.
Properties
- Don’t
@synthesize
properties. Modern objective-c does this for us automatically. - Always start with a lower case letter.
NSString
properties should always becopy
IBOutlets
should always beweak
Other readings
These are some good references / starting points for creating your own style guide or just to see other coding styles.


Love-O Meter
Events
Episodes
Companion
Closet
Inventory
Library
Mini Games
Shop
Recharge
Things that we should adapt?
Bubble Chat
Dialogue
Interactive Scene
Interactive Scene
Things that we should not adapt?
Mini-Games
Alternative to Mini-Games
Closet


PIE-EYED
World Championship Scotch Pie Awards 2019: Hungry Scottish Sun man on a munch mission to find the winning pie
by Graham MannAS a crusty old reporter with a bit of a gut I’ve been teased with the odd jibe of “Who ate all the pies?”
Now, I can happily confirm that yes, it was indeed me.
I’ve honed my taste buds at countless footie matches up and down the country for the best part of three decades.
And when I’m pie-eyed after a few pints I love nothing more than to tackle a steak bake.
In fact, I dread to think how much grease has dribbled down my arm over the years — but I reckon it could fill a good-sized Scottish Cup or three.
To get the chance to become an expert on my favourite subject seemed no more than pie in the sky.
So I was literally drooling when I was invited to join the seasoned pros judging contenders at the World Championship Scotch Pie Awards.
But my self-appointed authority quickly turned to mince.
It was a meaty learning curve that started with a word of caution from my judging team-mate Simon Young, a pie guru who’s been at 19 of the 21 annual competitions run by Scottish Bakers.
He warned: “This is a serious responsibility — bakers and butchers put a lot of time and effort into it.”
Words of wisdom from Simon — and our expert team leader — taught me there was more to judging pies than wolfing them down before unleashing a satisfied burp.
We mulled over a raft of characteristics such as ‘the bake’ and ‘boil out’ as well as shape, texture, taste and the filling-to-pastry ratio.
Before I knew it, I had set aside my carnivorous instinct of scooping dollops into my mouth and was now carefully wafting each pie’s aroma towards my twitching nostrils with a pretentious pinky stuck out.
I’m pretty sure it’s a look that would not go down well with your average footie punter.
But I’m absolutely certain they would give every one of the pies I tasted a resounding seal of approval.
The identity of the artisans behind the 450 bakery products showcased this week at Carnegie Conference Centre in Dunfermline remains a closely guarded secret.
The winners will be announced at a glittering awards ceremony in January when guests will tuck into pie, beans and chips served up by last year’s champ, The Little Bakery.
Alasdair Smith, chief executive of Scottish Bakers, revealed: “The top prize — to be named the World Scotch Pie Champion — is the single most coveted prize among pie-makers across the country.”
I will happily raise a Scotch pie — or two — to that.


This is an RDFa-based representation of the schema.org schema, the underlying representation of the schema.org vocabulary.
It is represented in a form based on W3C RDF/RDFS. We encourage proposals for schema.org improvements to be expressed in this same style. See the how we work document for information on collaboration.
See datamodel for more details, the developers page for alternate formats.
Note: the style of RDFa used here may change in the future. To see the substantive content of the schema, view the HTML source markup. We use a simple subset of RDFa for syntax, including prefixes that are declared in the RDFa initial context. We also use Markdown syntax within comments to make hypertext documentation easier to edit. Other formats are available.


Preparation time
less than 30 mins
Cooking time
30 mins to 1 hour
Serves
Makes 4 large fishcakes
Traditional fishcakes are delicious and easy to make. Pair with a simple cheese sauce for a comforting supper.
Place the hake into a large pan and season with sea salt and freshly ground black pepper. Pour over the milk and add the bay leaf, then cover the pan with aluminium foil and gently poach the fish over a medium low heat for 25 minutes, or until the fish is cooked through (the flesh should be opaque and flake easily).
Set the fish aside to cool, then flake the flesh into a bowl and discard the bones. Strain the poaching liquid into a measuring jug, discarding any solids. Add enough milk to the liquid to bring it up to 500ml/17½fl oz, then set aside for making the cheese sauce later.
In a large bowl, carefully fold together the fish, mashed potatoes, one beaten egg and the parsley until well combined. Season, to taste, with salt and freshly ground white pepper.
With damp hands, divide the mixture into four equal portions and form into patties. Dust the fishcakes in the flour, dip into the remaining beaten egg and roll in the breadcrumbs.
Heat a few tablespoons of vegetable oil in a frying pan and fry the fish cakes for 2-3 minutes on both sides, or until golden-brown and crisp all over.
For the cheddar cheese sauce, melt butter in a pan set over a medium heat, then beat in the flour. Cook the mixture for 2-3 minutes, then gradually whisk in the reserved milk mixture until smooth. Cook for 10-12 minutes, or until the sauce is thickened slightly, then stir in the grated cheddar cheese until melted. Season, to taste, with salt and freshly ground black pepper.
To serve, spoon the cheddar cheese sauce over the fishcakes.


Stories
Sustaining her vision
UC Santa Cruz professor of computer science Darrell Long and his wife, Mary Katherine Long, were high school sweethearts. Long’s companion for 38 years, she was a force of nature. The only daughter of a park ranger, she lived in various communities from San Diego to Eureka.
She loved camping with her two sons and riding a motorcycle. But she was especially passionate about the education and equality of women.
“Mary felt very strongly that educated women were the foundation of a civil and just society,” Long said.
Mary Long was deeply troubled by the fact that many women from underprivileged backgrounds face barriers to education and entry into lucrative STEM careers.
Mary’s death at age 53 was a great shock to Long and the couple’s children. Soon after her death, he decided to commemorate his wife by establishing the Mary Katherine Long Endowed Scholarship Fund, which will help low-income women at UC Santa Cruz pursue engineering and science educations.
Gifts to the scholarship have reached $100,000, but supporters hope it will grow much larger.
“I want the money to go to people who really need it: the single mom, the re-entry student who deferred college to support her family, or a student from a country where women are not treated as equals,” Long said. “I want to sustain her vision for years to come.”


Welcome to my website
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There are a few different issues to consider when tuning the performance of Berkeley DB transactional applications. First, you should review Access method tuning, as the tuning issues for access method applications are applicable to transactional applications as well. The following are additional tuning issues for Berkeley DB transactional applications:
Consider decreasing the level of isolation of transaction using the DB_READ_UNCOMMITTED, or DB_READ_COMMITTED flags for transactions or cursors or the DB_READ_UNCOMMITTED flag on individual read operations. The DB_READ_COMMITTED flag will release read locks on cursors as soon as the data page is nolonger referenced. This is also called degree 2 isolation. This will tend to block write operations for shorter periods for applications that do not need to have repeatable reads for cursor operations.
The DB_READ_UNCOMMITTED flag will allow read operations to potentially return data which has been modified but not yet committed, and can significantly increase application throughput in applications that do not require data be guaranteed to be permanent in the database. This is also called degree 1 isolation, or dirty reads.
During configuration, Berkeley DB selects a mutex implementation for the architecture. Berkeley DB normally prefers blocking-mutex implementations over non-blocking ones. For example, Berkeley DB will select POSIX pthread mutex interfaces rather than assembly-code test-and-set spin mutexes because pthread mutexes are usually more efficient and less likely to waste CPU cycles spinning without getting any work accomplished.
For some applications and systems (generally highly concurrent applications on large multiprocessor systems), Berkeley DB makes the wrong choice. In some cases, better performance can be achieved by configuring with the --with-mutex argument and selecting a different mutex implementation than the one selected by Berkeley DB. When a test-and-set spin mutex implementation is selected, it may be useful to tune the number of spins made before yielding the processor and sleeping. This may be particularly beneficial for systems containing several hyperthreaded processor cores. For more information, see the DB_ENV->mutex_set_tas_spins() method.
Finally, Berkeley DB may put multiple mutexes on individual cache lines. When tuning Berkeley DB for large multiprocessor systems, it may be useful to tune mutex alignment using the DB_ENV->mutex_set_align() method.


QET Solutions Ltd
Contact Information
Visit us in our office. You are most welcomed.
Thika Business Center 5th Floor, Suite 1 Thika,
<EMAIL_ADDRESS>Our office Number. Operational from Monday- Sat, 8.05am-5.30pm.
254 741 210 049


if you want to make the world a better place take a look at yourself and then make change
shaheenaz's website


Id: 305
Name: Scary Glenn
Status: Alive
Species: Humanoid
Type: Monster
Gender: Male
OriginName: Mr. Goldenfold's dream
OriginUrl: https://rickandmortyapi.com/api/location/18
LocationName: Mr. Goldenfold's dream
LocationUrl: https://rickandmortyapi.com/api/location/18
Image: https://rickandmortyapi.com/api/character/avatar/305.jpeg
Episode: ['https://rickandmortyapi.com/api/episode/2']
Url: https://rickandmortyapi.com/api/character/305
Created: 2018-01-05T14:11:53.287Z


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--- layout: post status: publish published: true title: The Future Shines During Cubs Intrasquad Game author: display_name: Corey Fineran login: Corey email<EMAIL_ADDRESS>url: '' author_login: Corey author_email<EMAIL_ADDRESS>wordpress_id: 6804 wordpress_url: http://ivyenvy.com/?p=6804 date: '2012-03-03 08:42:14 +0000' date_gmt: '2012-03-03 14:42:14 +0000' categories: - Outfield - The Cubs - Spring Training tags: - Brett Jackson - Peoria - Daytona - Matt Szczur - Hohokam Stadium - Fitch Park - Tony Campana - Baseball America - David DeJesus - Travis Wood - Tennessee - Jim Callis comments: - id: 5427 author: ryanativyenvydotcom author_email<EMAIL_ADDRESS>author_url: http://firstorderhistorians.wordpress.com date: '2012-03-06 12:43:27 +0000' date_gmt: '2012-03-06 18:43:27 +0000' content: Someone should ask Matt Szczur if he'd like to buy a vowel. Jeezum crow... ---
The Cubs left Fitch Park for Hohokam and the Spring Training schedule. Before the Cubs start exhibition play on Sunday vs. Oakland, they are conducting two intrasquad games at Hohokam. The players were split into basically an A Team (the Cubs of the present) and a B team (the Cubs of the future). The Cubs of the future seized the opportunity and made those of us that have put our hopes in the minor league players look like we know what we're talking about...for a day, at least.
Brett Jackson will probably not break camp with the Cubs, but we should see him occupying an outfield spot in front of the ivy sometime this year. Jackson led the game off with a home run and ended the game 2-2 with two walks, two RBIs, two runs scored and the HR.
Travis Wood, who came from the Reds in the Sean Marshall trade, served up that home run to Jackson and didn't pitch particularly well. He gave up six runs in three innings. Jackson wasn't the only prospect that had Wood's number on Friday. Matt Szczur, the former Villanova wide receiver, took Wood deep for a grand slam.
While the intrasquad game was not broadcast, I'm guessing the grand slam was not the most impressive play from Szczur to see. He also scored from 2nd on a sacrifice fly to right fielder David DeJesus. This is the type of heads-up and aggressive play that excites me about Szczur. I saw him play early in the 2011 season with the Peoria Chiefs and witnessed him turn a routine base-hit to the left fielder into a double without even glancing at left field.
For those that see Tony Campana as the lone speed threat, Szczur possesses the speed to be ranked the Fastest Baserunner and Best Athlete by Jim Callis at Baseball America. While he's not anywhere close to being considered a "power-hitter", he definitely has more power than Campana. In 2011, between Peoria and Daytona, Szczur had 10 home runs.
While Brett Jackson is waiting in the wings and probably major league-ready, Szczur is a few years away. After shining with Peoria and making the Midwest League All-Star Game, Szczur struggled a bit in Daytona. I have not heard anything about where Szczur may start the 2012 season, but perhaps with a strong showing in Mesa this spring, Szczur could start things off in Tennessee.
While Friday's game was merely a scrimmage, many Cubs fans were hoping to see the "B squad" stick it to big leaguers. It's easier to have hope about the future than to face the possibility that the young guys have less promise than the current players we are ready to rid ourselves of. At least for one day, we can see some hope on the horizon in Brett Jackson and Matt Szczur occupying two spots of the outfield in Wrigley.


Berrara is a quiet town just outside sussex inlet. It has accomidation for all vacation styles, from camping to staying in a cabin. Berarra is also a great place to get away from busy city life or a change of pace. Berarra beach connects to a lagoon at high tide. This lagoon is home to small fish and is a warmer temerature than the ocean. The beach is also dog friendly, so feel free to bring your canine pal along!


+++ title = "Jackeline" slug = "jackeline" date = 2007-02-20T00:00:00+10:00 tags = ["eccentric-encounters", "hondurans", "karaoke", "singing"] locations = ["mexico/mexico-city"] draft = false summary = """
The taxi driver convinced me to stay at Hotel Reforma Avenue, instead of staying at a hostel. Despite being more expensive, however, this stay was definitely worth it, because fate arranged for me to meet Jackeline.
""" +++The taxi driver convinced me to stay at Hotel Reforma Avenue, instead of staying at a hostel. Despite being more expensive, however, this stay was definitely worth it, because fate arranged for me to meet Jackeline.
{{< galleryphoto "2007-02-20-00-00-00--with-jackie-in-mexico-city.jpg" >}}We checked in to the hotel at the same time, and then we decided to go and have dinner together. Dinner led to a bus and train ride around Mexico City at night, and a twilight tour of the Zocalo plaza; which in turn led to a trip to a karaoke bar in Zona Rosa, that lasted well into the night.
Jackeline was only in Mexico City (and in all of Mexico) for one night, and she was desperate to go salsa dancing. But, being Monday night, almost all of the city's venues were closed (despite us being in the world's biggest city!), and the karaoke was all that we could find. Nevertheless, it was good fun.
Jackeline spoiled me by acting as my translator. Without her, I would have been pretty much screwed.
One thing's for sure, though: my first night in Mexico City was a crazy, a jam-packed, and a totally unforgettable experience.


Objectives
The aim of the thesis (extended abstract) was
to implement three community finding algorithms – Louvain, Infomap and Layered Label
Propagation; to benchmark them using two synthetic networks – Girvan-Newman and Lancichinetti-Fortunato-Radicchi;
to test them in real networks, particularly, in one derived from a Staphylococcus aureus MLST dataset; to compare
visualization frameworks – Cytoscape.js and D3.js (using SVG and Canvas elements), and, finally, to make it all available online.
Algorithms
Louvain
Louvain is divided in 2 phases:
Modularity Optimization - At the beginning, the algorithm will randomly order all
nodes in the network such that, one by one, it will remove and insert them in a different community. This will
continue until no significant modularity's variation is verified (using equation below);
Community Aggregation - After finishing previous step, every node belonging to the same community is merged into a single
giant one and the links of the new network are the sum of the links connecting nodes from the same pair of communities.
Both steps are executed until modularity's variation is lower than an input value.
Infomap
Infomap considers 2 steps: Minimizing Description Length (using map equation) and
Community Aggregation. Although the implementation is similar to the Louvain algorithm, the optimizing function
is different:
Layered Label Propagation
LLP is a semi-supervised algorithm that is able to detect communities based on a set of nodes that is partially labeled or unlabelled.
Considering an unlabelled network, it starts by assigning a random community to each node. Then, at the beginning of each cycle, all nodes are considered
in a random order. Based on the equation below, the community that maximizes its value for a given node, it is the one that is assigned.
Being ki the number of nodes with label λi in the neighborhood of a given node and νi the total number in the whole graph with the same label. γ is the
resolution parameter that buffers the number of nodes belonging to a given community in the neighborhood, by its usual presence across the whole network.
This algorithm is equivalent to Label Propagation whenever γ is 0.


Driven by the Internet of Things, Worldpay has been keen to demonstrate how you can integrate payments into everyday objects. So, we created Worldpay Within, an embeddable payments agent that can be 'plugged' into your app or a smart device. It then lets you discover other devices and pay for that device’s service.
We’ve got a series of open source software development kits (SDKs) that lets you make and accept payments from a range of devices. We’ve got SDKs for node.js, Go, .NET, Java and Python 2.7 and 3. You can download these SDKs, get playing, configure your setup, and recommend changes to our open source libraries.
You might want to use Worldpay Within if you’re a startup company that’s creating technologies relating to the Internet of Things. Or perhaps you’re a hobby developer who likes creating innovative technologies in your spare time.
The Internet of Things (IoT) is an initiative to connect everyday items to the internet. It could be a car which needs to pay for fuel or some repairs, a fridge which needs to order some groceries.
It is estimated that there will be 6 billion devices connected to the IoT by the end of 2016 and 20 billion by 2020. Some of these devices will consume services from other devices for which a payment will be required.
By using a set of APIs, “Thing” developers will be able to integrate Worldpay Within into their IoT device, enabling the “Thing” to make and/or receive payments for services to and from other “Things”.
Worldpay Within orchestrates smart things talking to each other and paying for services.
There are four simple interactions that takes place with Worldpay Within: Discover, Select, Pay and Release.
Let's imagine that a car needs some fuel. It stops by a petrol station and broadcasts that it needs some fuel. The petrol station receives this signal, informs the car of how much fuel costs and what options are available, and once the shopper has agreed the price, then Worldpay will process the payment and inform the petrol station that it can fuel the car.
In 2016, Worldpay hosted the Payments & IOT Hackathon in which we wanted to take digital payments to the next level. In 2017, we're hosting another Hackathon in Romania, in which we release Worldpay Within.
Want to find out more? Head over to the Hackathons page.
Worldpay Within is open source, so why not give it a go yourself? You can find the GitHub library here.
It's still an alpha based experiment, but we're actively building new features (and bug fixes) and are concurrently working on evolving the security architecture so we can take real payments.
If you'd like to contribute to the project, head over to the Issues page to see how you can help. And, of course, we'd love to see what you can come up with, so why not become a contributor?
Worldpay Within's SDK is written in GoLang and runs on smart devices, including Raspberry Pi. It allows you to make and receive payments within the IoT. We've got wrappers in these languages:
If you've got any questions, or if you want to find out more, why not give us a shout at Innovation@Worldpay.com.


Kai is the Elemental Master of fire. So he is the Fire Ninja. He is Nya's brother. His father's name is Ray. And his mothers name is Maya. And wants to resurrect Lord Garmadon. Despite the Ninjas efforts Harumi successfully brings Garmadon. Kai ends up marooned in the Realm of Oni Dragons. He went with Cole. He also went with Jay.
Kai and his younger sister worked as blacksmiths in their father's blacksmith shop. They worked in that shop all their life until they met Master Wu. Kai learned Spinjitzu taught by wu. Battling the likes of the Serpentine. Fighting the likes of the Stone Army. After Zane's sacrifice to destroy the Golden Master he took a break before reuniting. And then to go rescue Zane on Chen's Island. Kai also went with Zane. Kai lastly went with de-aged Wu. Kai was a terrible black smith. Kai is the current Elemental Master of Fire. And Ninja of Fire. Nya's elder brother. And Ray and Maya's son and eldest child. He and his younger sister worked as blacksmiths in their father's blacksmith shop. All their life until they met Master Wu. With his guidance Kai learned Spinjitzu. And discovered his other teammates. Which are Cole, Jay, Zane, and Lloyd.
Kai grew closer to Skylor as they competed in the Tournament of Elements. Krux tried to convince Kai that Kai's parents were traitors. Kai and Nya reunited with their parents. And stopped Krux and Acronix from changing the future. They managed to track them through time. Kai and the Ninja help save the various dragons. Helped save the dragons from the Dragon Hunters. And help the now teenage Wu regain his confidence. Kai taught teenager Wu find is confidence. The rest helped him find his memories. With whom he embarked on many adventure. Such As: battling the likes of the Serpentine. And the Stone Army.
And stopped Krux and Acronix.
Before tehy defeated them Wu sent Kai and Nya back to the present.
While Wu ended up lost in the time.
Kai and the Ninja later watches over Princess Harumi after she lost her adopted parents.
They later discover that she secretly is the leader of the Sons of Garmadon.
Kai and the rest of the Ninja fight to defend their home.
Kai used his blacksmithing skills to reforge Golden Weapons.
He made the wepons using the Golden Armor.
And later defeats the Oni by using the Tornado of Creation.
With the other Ninja and Wu and Garmadon.
After Zane's sacrifice to destroy the Golden Master, the ninja parted ways before reuniting to go rescue Zane on Chen's Island. There, Kai grew closer to Skylor, one of the tournament contenders, as they competed in the Tournament of Elements. Ultimately, he allied with the other Elemental Masters to defeat Chen's Anacondrai warriors. After the war ended, Lloyd was possessed by Morro, who escaped the Cursed Realm and released a legion of ghosts. Kai and the ninja battled Morro and his forces before the Cursed Realm was destroyed. Wiki Fandom


All content on this site is in various states of progress or abandonment
Royal Historical Society Centenary Fellow (2019-20) based at the Institute for Historical Research and the Centre for Medieval and Early Modern Studies at the University of Kent.
I am a CHASE funded doctoral candidate based at the Centre for Medieval and Early Modern Studies (MEMS) at the University of Kent. After ten years as a painter and decorator I began my studies at the Open University before completing a BA in History at Kent. Subsequently I found my home during an MA at MEMS where I was granted a CHASE AHRC doctoral studentship in 2016.
As part of my CHASE studentship I completed a two-month funded placement at the National Archives using subpoena writs to accurately date over six hundred cases from the Court of Chancery in the late fifteenth century. I also work with ‘Up on the Downs’, a landscape-based Heritage Lottery Funded project based in the Dover District Area which is exploring how to engage the public with medieval heritage in the Dover area.
My thesis is an investigation of corruption and anti-corruption processes within the development of English government institutions from 1307 to 1348. This work looks at the negotiation of centralised and devolved authority and how this authority, when subverted by corrupt actors, affected the crown and its subjects. The thesis includes a database of over 2000 individual cases of wrongdoing collated from anti-corruption investigations carried out in the first half of the fourteenth century. I utilise data science methodologies to collect, analyse, and visualise networks of officials and their patrons. I am interested in corruption, digital approaches to the study of the medieval period, Irish history, North Sea Trade, and cricket.
An academic C.V. is available in PDF form here. Up to date as of September 2020.
This site is written in markdown using RStudio, the blogdown package, and Hugo. The content is pushed to Github and hosted by Netlify. If you are interested in using a similar approach I used a combination of various tutorials, easily discoverable through a simple search, and parts of this Youtuber’s guides which were very helpful.


Articles
The power of Online Communities: Innovative discourses about climate change on twitter
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Artificial Intellingence & Private Metadata: Barriers and oportunities for a shared economy future
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Fake news on the internet during the 2016 US election campaign: Changes of power in the network society
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Life cycle and ICT development on family enviroment
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Social vectors of cellphone adoption
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Public opinion on government surveillance after Snowden: From deniers to hackers
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Internet freedom: The new Common of social movements
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| # |
Ship Name |
Defect ID |
Component |
Raised On |
Severity |
Defect Detai |
Raised By |
Last Corrective Action |
System |
Repair Criteria |
Status |
| 1 |
Ship 1 |
001/19 |
Component 1 |
2019-01-13 |
Severity 1 |
Defect detail 1 |
Aloke Kantal |
Last Corrective Action 1 |
System 1 |
Repair Criteria 1 |
Open |
| 1 |
Ship 1 |
001/19 |
Component 1 |
2019-01-13 |
Severity 1 |
Defect detail 1 |
Aloke Kantal |
Last Corrective Action 1 |
System 1 |
Repair Criteria 1 |
Open |
| 2 |
Ship 2 |
002/19 |
Component 2 |
2019-01-04 |
Severity 2 |
Defect detail 2 |
Rupak Hazra |
Last Corrective Action 2 |
System 2 |
Repair Criteria 2 |
Open |
| 3 |
Ship 3 |
003/19 |
Component 3 |
2019-01-25 |
Severity 3 |
Defect detail 3 |
Jayanta Kumar Das |
Last Corrective Action 3 |
System 3 |
Repair Criteria 3 |
In-progress |
Showing 50 - 100 of 500 entries


class Sass::Tree::Visitors::Base
The abstract base class for Sass visitors. Visitors should extend this class, then implement `visit_*` methods for each node they care about (e.g. `visit_rule` for {RuleNode} or `visit_for` for {ForNode}). These methods take the node in question as argument. They may `yield` to visit the child nodes of the current node.
Note: due to the unusual nature of {Sass::Tree::IfNode}, special care must be taken to ensure that it is properly handled. In particular, there is no built-in scaffolding for dealing with the return value of `@else` nodes.
@abstract
Public Class Methods
Runs the visitor on a tree.
@param root [Tree::Node] The root node of the Sass tree. @return [Object] The return value of {#visit} for the root node.
# File lib/sass/tree/visitors/base.rb, line 23 def self.visit(root) new.send(:visit, root) end
Protected Class Methods
Returns the name of a node as used in the `visit_*` method.
@param [Tree::Node] node The node. @return [String] The name.
# File lib/sass/tree/visitors/base.rb, line 59 def self.node_name(node) Sass::Util.deprecated(self, "Call node.class.node_name instead.") node.class.node_name end
Protected Instance Methods
Runs the visitor on the given node. This can be overridden by subclasses that need to do something for each node.
@param node [Tree::Node] The node to visit. @return [Object] The return value of the `visit_*` method for this node.
# File lib/sass/tree/visitors/base.rb, line 34 def visit(node) if respond_to?(node.class.visit_method, true) send(node.class.visit_method, node) {visit_children(node)} else visit_children(node) end end
Visit the child nodes for a given node. This can be overridden by subclasses that need to do something with the child nodes’ return values.
This method is run when `visit_*` methods `yield`, and its return value is returned from the `yield`.
@param parent [Tree::Node] The parent node of the children to visit. @return [Array<Object>] The return values of the `visit_*` methods for the children.
# File lib/sass/tree/visitors/base.rb, line 51 def visit_children(parent) parent.children.map {|c| visit(c)} end
`yield`s, then runs the visitor on the `@else` clause if the node has one. This exists to ensure that the contents of the `@else` clause get visited.
# File lib/sass/tree/visitors/base.rb, line 66 def visit_if(node) yield visit(node.else) if node.else node end