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Irreverent, unapologetically arrogant and uncensored, IT Professional Services industry veteran Jason Perlow muses on a cornucopia of topics on all matters of Information Technology.

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The robots are coming! Greg Nichols covers robots and automation from a human perspective. You agree to receive updates, promotions, and alerts from ZDNet. High-molecular-weight DNA was extracted from one-week-old seedlings of 20 diverse barley accessions given in Supplementary Table 10 , using a previously described large-scale DNA extraction protocol The bp paired-end libraries for other accessions, bp paired-end libraries and mate-pair libraries of three sizes were prepared and sequenced at the University of Illinois Roy J.

Carver Biotechnology Center. For the other accessions, in situ Hi-C libraries were prepared using a previously described method Sequencing data generated from each of the libraries are given in Supplementary Table Libraries were pooled at equimolar concentrations, quantified by qPCR and paired-end-sequenced on an Illumina HiSeq for cycles. The data generated for each tissue are given in Supplementary Table 2.

Equimolar concentration of each fraction were pooled, and a minimum of one microgram of double-stranded cDNA was used for Iso-Seq library construction as per the PacBio library construction protocol.

The steps involved in Iso-Seq data analysis were the generation of circular consensus sequences, and then the classification of circular consensus sequence reads into full-length non-chimeric reads and non-full length reads on the basis of the presence of primer sequences and polyA sequences.

Full-length non-chimeric reads were then clustered on the basis of sequence similarity to yield high- and low-quality isoforms. The data generated and method of library preparation are given in Supplementary Table 2.

Gene models for Morex, Barke and HOR were predicted using transcriptome data Supplementary Table 2 and protein homology evidence, and derived by a previously described annotation pipeline 5. High-confidence gene models from these accessions were aligned to pseudo-chromosomes of each accession separately using blat For each genomic region identified by blat, additional alignments were performed by exonerate 46 in its genomic neighbourhood ranging between 20 kb upstream and 20 kb downstream of the match position.

A series of quality criteria was applied to select high-confidence gene models in each accession. The functional annotation for genes of 20 accessions was carried out using the AHRD pipeline v. Orthologous gene groups between the twenty accessions were predicted using OrthoFinder 47 v.

To obtain a consistent transposon annotation across all lines for transposons and tandem repeats, the same methods were applied to all 20 barley lines.

To remove overlapping annotations, the vmatch output was filtered for redundant hits via a priority-based approach. The resulting transposon annotations are overlap-free, but disrupted elements from nested insertions have not been defragmented into one element.

Still-intact full-length LTR retrotransposons were identified with LTRharvest 49 , a program that scans the genome for LTR retrotransposon specific structural hallmarks, such as long terminal repeats, RNA cognate primer binding sites and target site duplications.

LTRharvest included in genometools 1. The inner domain order served as a criterion for the LTR-retrotransposon superfamily classification into either Gypsy or Copia. In the cases of insufficient domain information, the elements were assigned as still undetermined. Most of the transposons insert at random locations leading to novel and usually unique sequence stretches at both borders around the inserted element and the neighbouring original sequence.

The de novo detected full-length LTR set provides defined element borders, a prerequisite for the exact positioning of transposable element junctions. We used bp single transposable element junctions with 50 bp outside and 50 bp inside the element from both sides of the element and merged them to bp joined junctions per element.

Junctions from the reverse strand were reverse-complemented. By including sequence information outside of the element, the repetitiveness of high-copy transposable element families is removed and at the same time the syntenic context is provided even for elements located on chrUn that is, not assigned to chromosomal pseudomolecules. Owing to higher sensitivity in detecting deletions over insertions, a paired genome alignment strategy was used in which each assembly was aligned to reference genome Morex reciprocally by treating Morex as a query and reference using Minimap2 v.

From these two alignments, insertion and deletions were called using Assemblytics v. Then, only deletions were selected in both alignments and converted into PAVs with regard to Morex. Mosdepth v. PAVs overlapping with single copy regions were identified by BedTools v. Based on masking, single-copy regions in each assembly were obtained in. Single-copy sequences from all the assemblies were combined to perform an all-against-all blast search.

A representative from each cluster the largest contained sequence was selected and used for estimating pan-genome size. Clusters shared by all the 20 accessions are referred to as the core genome, and clusters with sequences originating from 1 to 19 genotypes are considered as the variable genome. In situ Hi-C libraries were prepared from one-week-old seedlings of barley IPK core50 collection 9 Supplementary Table 5 based on a previously described protocol 43 Sequencing, Hi-C raw data processing and inversion calling were performed as previously described 34 using the MorexV2 reference genome sequence assembly 6.

The breakpoint regions were identified by pairwise genome alignment using Minimap2 v. Raw reads Supplementary Table 4 were trimmed with cutadapt v. The alignments were sorted using Novosort V3. BCFtools v. Previously generated genotyping-by-sequencing data 9 were aligned to the MorexV2 reference and identified SNPs using a previously described variant calling pipeline 9.

In total, 38 F 2 plants from the direct cross and individual heads from F 3 seeds were progressed to the F6 generation by single seed descent method. The F 6 recombinant inbred lines RIL in total were used for construction of a genetic linkage map. Genomic DNA was extracted from the leaves of a single plant per RIL using the cetyl-trimethyl-ammonium bromide method. Sequences flanking polymorphisms detected by DArT-seq were aligned against the MorexV2 genome assembly to determine their physical positions Supplementary Table 7.

The distance between South Perth and Shepperton is over 3, km. The Merredin site is located inland and receives little rainfall, whereas the Gibson site receives a high amount of rainfall: the other sites are in between. The experimental design for field trial sites was performed as previously described In brief, all regional field trials partially replicated design were planted in a randomized complete block design using plots of 1 by 5 m 2 , laid out in a row—column format and the middle 3 m was harvested for grain yield.

Field trials in South Perth and Shepperton were conducted using double rows with a cm distance within and between rows, owing to space constraints.

Seven control varieties were used for spatial adjustment of the experimental data. Measurements were taken at each plot of each field experiment in the study to determine flowering time days to Zadoks stage ZS 49 , plant height and grain yield.

Plant height was determined by estimating the average height from the base to the tip of the head of all plants in each plot. Local best practices for fertilization and disease control were adopted for each trial site. The genotypic data, phenotypic data and genetic map were formatted and imported to MapQTL6. Interval mapping was conducted for each trait, and then the markers with a logarithm of odds LOD value of above 3.

If the markers with the highest LOD value were inconsistent with the cofactor markers, then the new markers were selected as cofactors and re-calculated.

The QTL results and charts were exported from the software. A total of Before use, Illumina fragment reads were screened for phix contamination. The final read set consists of ,, reads, representing a total of The initial assembly was generated by assembling 32,, PacBio reads This produced an initial assembly of 1, scaffolds 1, contigs , with a contig N50 of A first round of breaking chimeric scaffolds was done using the POPSEQ genetic map 19 to identify contigs bearing markers from distant genomic regions.

A total of 17 misjoins were identified and resolved. A total of 59 homozygous SNPs and 15, homozygous indels were corrected. After these correction steps, the assembly contains 4, Published Hi-C data of the Morex cultivar was used 5. Full-length cDNA sequences 44 were aligned to the assemblies to assess gene space completeness. Whole-genome assemblies were done with Minimap2. Structural variant calling with Assemblytics v. Further information on research design is available in the Nature Research Reporting Summary linked to this paper.

All raw sequence data collected in this study and sequence assemblies have been deposited at the European Nucleotide Archive ENA. Bayer, P. Plant pan-genomes are the new reference. Plants 6 , — PubMed Google Scholar. Dawson, I. Barley: a translational model for adaptation to climate change. New Phytol. Stein, N. The Barley Genome Springer, International Barley Genome Sequencing Consortium.

A physical, genetic and functional sequence assembly of the barley genome. Nature , — ADS Google Scholar. Mascher, M. A chromosome conformation capture ordered sequence of the barley genome. Monat, C. Genome Biol. Mapping-by-sequencing accelerates forward genetics in barley.

Russell, J. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Milner, S. Genebank genomics highlights the diversity of a global barley collection.

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Taketa, S. Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Natl Acad. USA , — Tettelin, H. Ho, S. Structural variation in the sequencing era. Danilevicz, M. Plant pangenomics: approaches, applications and advancements. Plant Biol. Prospects of pan-genomics in barley. Coronado, M. Immature pollen-derived doubled haploid formation in barley cv.

Golden Promise as a tool for transgene recombination. Once MacPorts is installed, these commands will install the required dependent packages:. Things may also work under Cygwin, but that is not the preferred windows environment. Building with MinGW64 is not supported. Unzip it in the directory that you want SIMH to reside in. Unpack it and set the file attributes as follows:.

The simh-vms-pcap. For example, if these exist here:. Then the following should exist: [-. COM [-. Skip to content. Star 1. The Computer History Simulation Project simh.

Branches Tags. Could not load branches. Could not load tags. Latest commit. Git stats 4, commits. Failed to load latest commit information. Aug 10, Dec 11, Oct 23, Sep 2, Oct 11, Apr 19, BESM6: Implemented punched card input and punched tape output. Jan 2, Nov 1, I Compiler warning cleanup. Oct 19, Dec 2, Apr 11, ID Fix DP unit busy test.

Jul 22, Jun 8, Nov 7, PDP8: Fix device conflict warnings to report problems correctly. S3: Provide readable 7 segment error code display. Jul 21, SCSI: Add tape activity specific debug option. Sep 6, Visual Studio Projects.

Aug 24, Jun 22, PDP Cleanup potential compiler warnings. My theory is that perl2exe uses smarter tree pruning logic than PAR::Packer , but that's pure speculation. If you have access to perl2exe, you can use it to create a tight Windows executable.

See lines in the cloc source code for a minor code modification that is necessary when using perl2exe. Finally, invoke the newly installed pp command with the cloc souce code to create an. The Strawberry Perl derived executable on the SourceForge download area was created with the portable version on a Windows 7 computer. Here's an example of running cloc against the Perl v5. To run cloc on Windows computers, one must first open up a command aka DOS window and invoke cloc.

The above list can be customized by reading language definitions from a file with the --read-lang-def or --force-lang-def options. Languages with file extension collisions are difficult to customize with --read-lang-def or --force-lang-def as they have no mechanism to identify languages with common extensions. In this situation one must modify the cloc source code.

Next, attempt to determine whether or not found files contain recognized computer language source code. Finally, for files identified as source files, invoke language-specific routines to count the number of source lines. The options modify the algorithm slightly. The --read-lang-def option for example allows the user to read definitions of comment filters, known file extensions, and known scripting languages from a file. The code for this option is processed between Steps 2 and 3.

How can you tell if cloc correctly identifies comments? One way to convince yourself cloc is doing the right thing is to use its --strip-comments option to remove comments and blank lines from files, then compare the stripped-down files to originals. The extention argument given to --strip-comments is arbitrary; here nc was used as an abbreviation for "no comments".

We can now compare the orignial file, sqlite3. A rigorous proof that the stripped-down file contains the same C code as the original is to compile these files and compare checksums of the resulting object files. Versions of cloc before v1. Beginning with v1. At the moment the automatic extraction method works reasonably well on Unix-type OS's for the following file types:.