20210130

Contents
  1. 1. Working directories
  2. 2. test-sra
  3. 3. Revision of p62 draft (11:00)
  4. 4. PDB Gallery
  5. 5. PubChem
    1. 5.1. Ref
  6. 6. NFE2L2 (nuclear factor, erythroid 2 like 2)
  7. 7. BioGPS - your Gene Portal System
  8. 8. ‘Authentication Required’ window. : gnome
  9. 9. Convert html to pdf
    1. 9.1. wkhtmltopdf
    2. 9.2. weasyprint
  10. 10. RStudio/Package update
  11. 11. SRA Analysis

Working directories

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i=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/05_00_HFMD
pcmanfm -n ${i}; cd {i} # Examining COVID-19 Forecasting using Spatio-Temporal Graph Neural Networks
#
i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_2
pcmanfm -n ${i}; cd {i} # Draft pack of "p62_Draft_20210129_wj.7z" from Wang Jiao
#
i=/media/${USER}/ht_5T/Work/References/Computer_Tips/Linux_Tips/Not_Classified/PDF_Learning.Rmd; subl ${i} # update
  1. Received “Expression of Human Skin-Specific Genes Defined by Transcriptomics and Antibody-Based Profiling” from Guo Yifan.
  2. Received “Examining COVID-19 Forecasting using Spatio-Temporal Graph Neural Networks” from Ji Tianjiao.
  3. Draft pack of “p62_Draft_20210129_wj.7z” from Wang Jiao

test-sra

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cat SRR.list | xargs -I % test-sra % > `date +%Y%m%d_%H%M`.xml
xml2 < File.xml > File.txt
#
# SRR11819915 SRR11819916 SRR11819917 SRR11819918 SRR11819919 SRR11819920 SRR11819921 SRR11819922 SRR11819923 SRR11819924 SRR11819925 SRR11819926 SRR11819927 SRR11819928 SRR11819929 SRR11819930 SRR11819931 SRR11819932 SRR11819933 SRR11819934 SRR11819935 SRR11819936 SRR11819937 SRR11819938 SRR11819939 SRR11819940 SRR11819941 SRR11819942 SRR11819943 SRR11819944 SRR11819945 SRR11819946 SRR11819947 SRR11819948 SRR11819949 SRR11819950 SRR11819951 SRR11819952 SRR11819953 SRR11819954 SRR11819955 SRR11819956 SRR11819957 SRR11819958 SRR11819959 SRR11819960 SRR11819961 SRR11819962 SRR11819963 SRR11819964 SRR11819965 SRR11819966

Revision of p62 draft (11:00)

  1. Powerpoint review. Comments for Figure 3 sent to Wang Jiao via QQ.
  2. Draft review
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i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Rev_2/p62_Draft_20210129_2200.docx
setsid wps ${i}

PDB Gallery

Myoglobin

No crystal data of Nrf2 in PDB.

PubChem

Ref

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8874304.pdf
#
3829568.epub
kft172.pdf
  • tBHQ-Overview_of_Multiple_Mechanisms_against_Oxidative_Stress_for_Attenuating_Methamphetamine-Induced_Neurotoxicity.pdf
  • The_Nrf2_Activator_tBHQ_Differentially_Affects_Early_Events_Following_Stimulation_of_Jurkat_Cells.epub
  • The_Nrf2_Activator_tBHQ_Differentially_Affects_Early_Events_Following_Stimulation_of_Jurkat_Cells.pdf

NFE2L2 (nuclear factor, erythroid 2 like 2)

BioGPS - your Gene Portal System

  • Need to learn more
  • CSV document for expression pattern (multiple datasets with different probe, included)

‘Authentication Required’ window. : gnome

Convert html to pdf

wkhtmltopdf

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sudo apt-get install wkhtmltopdf
#
wkhtmltopdf file.html file.pdf

weasyprint

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weasyprint input.html output.pdf
#
i=
weasyprint ${i} ${i%.html}.pdf

RStudio/Package update

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sudo -i R
#
# code as below run in R
#
install.packages(c("backports", "BH", "boot", "brio", "broom", "caTools", "class", "cli", "clusterGeneration", "codetools", "colorspace", "cpp11", "crosstalk", "data.table", "DBI", "dbplyr", "deldir", "diffobj", "dplyr", "DT", "expm", "fansi", "fastmap", "fda", "forcats", "foreign", "fpc", "future", "ggplot2", "ggvis", "gh", "git2r", "globals", "gridGraphics", "hexbin", "hms", "htmltools", "htmlwidgets", "httpuv", "hunspell", "inline", "isoband", "jsonlite", "knitr", "lubridate", "magrittr", "Matrix", "matrixStats", "mclust", "MCMCglmm", "memoise", "microdemic", "nlme", "nnet", "PBSmapping", "pillar", "pixmap", "pkgbuild", "plotly", "plotrix", "pracma", "prettydoc", "processx", "ps", "qpcR", "quantreg", "rappdirs", "raster", "Rcpp", "RcppArmadillo", "RcppEigen", "rentrez", "reprex", "rgdal", "rgl", "rJava", "rlang", "rmarkdown", "robustbase", "rprojroot", "rstudioapi", "segmented", "seqinr", "sf", "shiny", "shinythemes", "slam", "sp", "spam", "spatial", "spatstat.data", "spatstat.utils", "spdep", "storr", "tensorA", "testthat", "tibble", "tinytest", "tinytex", "tm", "tufte", "usethis", "V8", "vctrs", "vegan", "waldo", "withr", "xfun", "XLConnect"))
#
1: In install.packages(c("backports", "BH", "boot", "brio", "broom",  :
  installation of package ‘rJava’ had non-zero exit status
2: In install.packages(c("backports", "BH", "boot", "brio", "broom",  :
  installation of package ‘rgdal’ had non-zero exit status
3: In install.packages(c("backports", "BH", "boot", "brio", "broom",  :
  installation of package ‘sf’ had non-zero exit status
4: In install.packages(c("backports", "BH", "boot", "brio", "broom",  :
  installation of package ‘XLConnect’ had non-zero exit status
5: In install.packages(c("backports", "BH", "boot", "brio", "broom",  :
  installation of package ‘spdep’ had non-zero exit status
6: In install.packages(c("backports", "BH", "boot", "brio", "broom",  :
  installation of package ‘qpcR’ had non-zero exit status
#
i <- "backports"
install.packages(i)
#
sudo R CMD javareconf

SRA Analysis

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# Reference sequences
DB_Path=/home/ht/Downloads/DB/
#
Ref=${DB_Path}Truncated_Rev/HLA-G_RNA_Truncated_Rev.fas
Ref=${DB_Path}Gender/hSRY_NC_000024.fasta
Ref=${DB_Path}Gender/Gender_Determinant_cDNA_Sum.fas
Ref=${DB_Path}Essential/Essential.fas
Ref=${DB_Path}Genome/Genomic_DNA_Divided.fas
Ref=${DB_Path}Exon/HLA-G_Exon_Sum.fasta
Ref=${DB_Path}Genome_LNG/HLA-G_gDNA_NG_029039_Divided.fasta
Ref=${DB_Path}RefRNA/Essential.fas
Ref=${DB_Path}RefRNA/HLA-G_Exon_Truncated_Sum.fasta
Ref=${DB_Path}RefRNA/HLA-G_gDNA_NG_029039_Divided.fasta
Ref=${DB_Path}RefRNA/HLA-G_Exon_Sum.fasta
Ref=${DB_Path}RefRNA/HLA-G_cDNA_Variant.fas
Ref=${DB_Path}RefRNA/hSRY_NC_000024.fasta
Ref=${DB_Path}RefRNA/Gender_Determinant_cDNA_Sum.fas
Ref=${DB_Path}RefRNA/HLA-G_RefRNA.fasta
Ref=${DB_Path}RefRNA/Genomic_DNA_Divided.fas/
Ref=${DB_Path}RefRNA/HLA-G_RNA_Truncated_Rev.fas
Ref=${DB_Path}RefRNA_Rev/HLA-G_cDNA_Variant.fas
Ref=${DB_Path}Truncated/HLA-G_Exon_Truncated_Sum.fasta

Expand all items >>

20210129

Contents
  1. 1. Working directories
  2. 2. Move documents in BaiduNetDisk
  3. 3. SRA Analysis
    1. 3.1. SRP262513 (SRA Study)
      1. 3.1.1. Procedures
      2. 3.1.2. Characterisation of Ovarian Cancer Cell Line NIH-OVCAR3 and Implications of Genomic, Transcriptomic, Proteomic and Functional DNA Damage Response Biomarkers for Therapeutic Targeting
        1. 3.1.2.1. RNA-Seq
  4. 4. SRA (Sequence Read Archive)

Working directories

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i=/media/ht/ht_5T/Work/肿瘤室工作/日常管理/组会/周一科室会/20201221
pcmanfm -n ${i}; cd ${i} # Backup of Powerpoint document
#
i=/media/ht/ht_5T/Work/References/Computer_Tips/Office_Tips/Excel/Agenda
pcmanfm -n ${i}; cd ${i} # Agenda in Excel format
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA
pcmanfm -n ${i}; cd ${i} # HLA-G analysis
#
i=/media/ht/ht_5T/eBooks/网络小说
pcmanfm -n ${i}; cd ${i} # [藏地密码.7z](/media/ht/ht_5T/eBooks/网络小说/藏地密码.7z)
#
i=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/09_02_63_HEV/HEV_Notes_20210129_1610.docx
setsid wps ${i} # Revised document for Yin Wenjiao
#
#########################################################
########### E-MTAB-1733 ###################################
#########################################################
#
i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/E-MTAB-1733_Note.Rmd
subl ${i}
#
i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/
pcmanfm -n ${i}; cd ${i} # HLA-G in adults
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
pcmanfm -n ${i}; cd ${i} # SRA analysis
#
subl /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/README.sh
#
setsid wps /media/ht/ht_5T_5/HLA-G/SRA/Summary/HLA-G_Note_20210128_0818.docx
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axel https://download.anydesk.com/linux/anydesk_6.1.0-1_amd64.deb
#
wget -rnp https://download.anydesk.com/linux/

Move documents in BaiduNetDisk

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i=/media/ht/ht_5T/Work/References/Computer_Tips/Office_Tips/Excel/Agenda
pcmanfm -n ${i}; cd ${i} # Agenda in Excel format

Direcotry, resources

  • 1日程表【微信公众号：Word联盟】.xltx
  • 2日程表【微信公众号：Word联盟】.xltx
  • 3日程表【微信公众号：Word联盟】.xltm
  • 4日程表【微信公众号：Word联盟】.xltx
  • 5日程表【微信公众号：Word联盟】.xltx
  • 6日程表【微信公众号：Word联盟】.xltx

Cahnge to as below

  • 1日程表.xltx
  • 2日程表.xltx
  • 3日程表.xltm
  • 4日程表.xltx
  • 5日程表.xltx
  • 6日程表.xltx

SRA Analysis

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i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA
pcmanfm -n ${i}; cd ${i} # HLA-G analysis

Error

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Error: NCBI C++ Exception:
    T0 "/media/ht/ht_2T/Work/Bioinformatics/Bioinfo-Softs/NCBI/magicblast/ncbi-magicblast-1.2.0-src/c++/src/sra/readers/sra/vdbread.cpp", line 996: Error: ncbi::objects::CVDBColumn::Init() - Cannot get VDB column: /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/SRR11296728.sra.READ (0x31c5044a: file invalid while opening directory within file system module)

[bam_sort_core] merging from 1 files and 1 in-memory blocks...
^[[FError: NCBI C++ Exception:
    T0 "/media/ht/ht_2T/Work/Bioinformatics/Bioinfo-Softs/NCBI/magicblast/ncbi-magicblast-1.2.0-src/c++/src/sra/readers/sra/vdbread.cpp", line 996: Error: ncbi::objects::CVDBColumn::Init() - Cannot get VDB column: /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/SRR11296841.sra.READ (0x31c5044a: file invalid while opening directory within file system module)

SRP262513 (SRA Study)

  • SRR11819915.sra
  • SRR11819919.sra
  • SRR11819923.sra

SRR11819915_vs_HLA为空文件。

SRP262513.xlsx established. SRP262513.xlsx

**Current viewer** **Old version viewer**

Procedures

Characterisation of Ovarian Cancer Cell Line NIH-OVCAR3 and Implications of Genomic, Transcriptomic, Proteomic and Functional DNA Damage Response Biomarkers for Therapeutic Targeting

In order to be effective models to identify biomarkers of chemotherapy response, cancer cell lines require thorough characterization. In this study, we characterised the widely used high grade serous ovarian cancer (HGSOC) cell line NIH-OVCAR3 using bioinformatics, cytotoxicity assays and molecular/functional analyses of DNA damage response (DDR) pathways in comparison to an ovarian cancer cell line panel. Bioinformatic analysis confirmed the HGSOC-like features of NIH-OVCAR3, including low mutation frequency, TP53 loss and high copy number alteration frequency similar to 201 HGSOCs analysed (TCGA). Cytotoxicity assays were performed for the standard of care chemotherapy, carboplatin, and DDR targeting drugs: rucaparib (a PARP inhibitor) and VE-821 (an ATR inhibitor). Interestingly, NIH-OVCAR3 cells showed sensitivity to carboplatin and rucaparib which was explained by functional loss of homologous recombination repair (HRR) identified by plasmid re-joining assay, despite the ability to form RAD51 foci and absence of mutations in HRR genes. NIH-OVCAR3 cells also showed high non-homologous end joining activity, which may contribute to HRR loss and along with genomic amplification in ATR and TOPBP1, could explain the resistance to VE-821. In summary, NIH-OVCAR3 cells highlight the complexity of HGSOCs and that genomic or functional characterization alone might not be enough to predict/explain chemotherapy response.

Keywords: ATR; PARP; homologous recombination repair; non-homologous end-joining; ovarian cancer; platinum.

RNA-Seq

  • Cell pellets containing ~40,000 cells were collected of the 13 ovarian cancer cell lines (Table S3) including the NIH-OVCAR3 cells, and cryo-preserved and shipped for targeted RNA-Sequencing analysis by HTG Molecular Diagnostics Inc. (Tucson, AZ, USA). The samples were run on the Illumina NextSeq (Illumina, San Diego, CA, USA) with the HTG EdgeSeq Oncology biomarker panel assay (961–002) containing probes against 2567 genes including 15 housekeeper genes, and four negative and four positive process control genes. The HTG EdgeSeq Parser was used to align FASTQ files to probe list by the company. Following quality control, the raw read counts were estimated followed by estimation of read counts per million after median normalisation. The normalized gene expression for selected DDR genes was calculated by using expression of ACTB gene as the normalization control, which showed the least standard deviation of gene expression across cell lines. The data is accessible through GEO submission GSE150942 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150942).
  • RNA-Seq data (read counts) for NIH-OVCAR3 cell line was downloaded from the CCLE database
    (https://portals.broadinstitute.org/ccle/data).

SRA (Sequence Read Archive)

Expand all items >>

20210127

Contents
  1. 1. Working directories
  2. 2. Contract editing
    1. 2.1. 模板文件
  3. 3. Reinstallation of WPS in Lubuntu (Vision)
  4. 4. SRA download
  5. 5. KinhDown
    1. 5.1. Ref
  6. 6. magicblast with HLA-G series database

Working directories

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subl /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/README.sh
#
i=/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Drug_Test/20210125
pcmanfm -n ${i}; cd ${i}
#
i=/media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/KinhDown
pcmanfm -n ${i}; cd ${i} # [KinhDown](https://ubaq.lanzous.com/s/KinhDown)

Contract editing

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i=/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Drug_Test/20210125
pcmanfm -n ${i}; cd ${i}

需要根据最新模板进调整。

模板文件

附件2-参考模板-横向科研课题协议.doc
/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Drug_Test/20210125/附件2-参考模板-横向科研课题协议.doc

Reinstallation of WPS in Lubuntu (Vision)

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sudo dpkg -i /media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/WPS/Installer/wps-office_10.1.0.6757_amd64.deb # Vision Lubuntu

SRA download

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i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/
pcmanfm -n ${i}; cd ${i} 
#
subl /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/README.sh
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i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer
pcmanfm -n ${i}; cd ${i} 
#
prefetch SRR11296716 SRR11296723 SRR11296732 SRR11296751 SRR11296770 SRR11296787 SRR11296800 SRR11296802 SRR11296823 SRR11296836 SRR11296844 SRR11296845 SRR11296847 SRR11296869 SRR11296879 SRR11296882

List as below from Wang Jiao’s idea

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SRR11296716
SRR11296723
SRR11296732
SRR11296751
SRR11296770
SRR11296787
SRR11296800
SRR11296802
SRR11296823
SRR11296836
SRR11296844
SRR11296845
SRR11296847
SRR11296869
SRR11296879
SRR11296882

KinhDown

  • KinhDown

    • 有云参数获取器.exe
    • 云解析Cookie共享器.7z
    • Aria2.zip
    • KinhDown_版本2.3.74.7z
    • KinhDown公测版.apk
    • KinhDown[自动更新文件].exe
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i=/media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/KinhDown
pcmanfm -n ${i}; cd ${i} # [KinhDown](https://ubaq.lanzous.com/s/KinhDown)

Ref

magicblast with HLA-G series database

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mkdir Essential
cd Essential
#
DB="/home/ht/Downloads/DB/Essential/Human_Essential"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
cd /home/ht/Downloads/DB/SRA/
i=Exon
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Exon/HLA_Exon"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Genome
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Genome/HLA_Genome_Screen"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Genome_LNG
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Genome_LNG/HLA_Genome_LNG_Screen"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=RefRNA
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/RefRNA/HLA"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=RefRNA_Rev
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/RefRNA_Rev/RefRNA_Rev"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Truncated
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Truncated/HLA_Truncated"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/
#
i=Truncated_Rev
mkdir ${i}; cd ${i}
DB="/home/ht/Downloads/DB/Truncated_Rev/HLA_Truncated_Rev"
for SRA in ../*.sra; do magicblast -num_threads 6 -sra "${SRA}" -db ${DB} | samtools view -bS ->  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam"; samtools sort  "`basename ${SRA%.sra}`_vs_`basename ${DB}`.bam" > "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; samtools index "`basename ${SRA%.sra}`_vs_`basename ${DB}`.sort.bam"; done; cd /home/ht/Downloads/DB/SRA/

Expand all items >>

20210126

Contents
  1. 1. Working directories
  2. 2. SRR downloading for Wang Jiao
    1. 2.1. Ref
  3. 3. Download FASTA from the site as below to build human reference genome
    1. 3.1. Ref
  4. 4. Index (Content) in Hexo page
  5. 5. cat (output on a screen) a document without uncompressing in Mac OSX
  6. 6. ICTV
  7. 7. HEV Record from README.md
  8. 8. Comments in Rmd document
Content function introduced

Working directories

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i=/media/ht/ht_5T/Work/Projects/Other_Projects/Coronavirus_Project/Ref/NYT
pcmanfm -n ${i}; cd ${i} # Why_the_Covid_Vaccine_Rollout_Is_Not_Enough_to_Curb_Infections-The_New_York_Times.pdf
#
i=/media/ht/ht_5T/Work/Projects/NFE/B95-8/Summary/B95-8_Nrf2_20210126_1651.pptx
setsid wpp ${i}
#
i=/media/ht/ht_5T/Work/Projects/NFE/Summary/NFE2_Sum_Large.pptx
setsid wpp ${i} # Keap1 WB updated
#
i=/media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/QQ
pcmanfm -n ${i}; cd ${i} # Debian pack of QQ downloaded
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Summary/HLA-G_Note_20201226_2140.docx
setsid wps ${i} # p62 draft, content added # Info addition needed
# OneDrive uploaded

SRR downloading for Wang Jiao

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i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer
pcmanfm -n ${i}; cd ${i} 
#
prefetch SRR11296716 SRR11296723 SRR11296732 SRR11296751 SRR11296770 SRR11296787 SRR11296800 SRR11296802 SRR11296823 SRR11296836 SRR11296844 SRR11296845 SRR11296847 SRR11296869 SRR11296879 SRR11296882

Ref

Download FASTA from the site as below to build human reference genome

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axel ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz

Ref

Index (Content) in Hexo page

cat (output on a screen) a document without uncompressing in Mac OSX

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zcat < file
gunzip -c file

ICTV

HEV Record from README.md

  • README.md, /media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/09_02_63_HEV/README.md
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**HEV**

Unassigned  Hepeviridae     Orthohepevirus  Orthohepevirus A

Keyword='Orthohepevirus A'
ete3 ncbiquery --search ${Keyword} --info

# Taxid Sci.Name    Rank    Named Lineage   Taxid Lineage
1678141 Orthohepevirus  genus   root,Viruses,ssRNA viruses,ssRNA positive-strand viruses, no DNA stage,Hepeviridae,Orthohepevirus   1,10239,439488,35278,291484,1678141

Comments in Rmd document

  • Ctrl + Shift + C
  • >
  • #
  • <!-- your comment -->

Expand all items >>

20210125

Contents
  1. 1. Working directories
  2. 2. SRA Integrity check
  3. 3. 基于神经网络构建的戊型肝炎病毒时空分布模型的研究
  4. 4. Reading
  5. 5. Macro usage in Linux Office Suite (WPS or LibreOffice)

Working directories

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i=/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NCBI
pcmanfm -n ${i}; cd ${i} # SRA command/integrity check # ref to text as below
#
setsid wpp /media/ht/ht_5T/Work/Projects/NFE/Summary/NFE2_Sum_Large.pptx # add result of B95-8 treated with tBHQ
#
i=/media/ht/ht_5T/Work/DL/20210125
pcmanfm -n ${i}; cd ${i} # organize/clean-up documents  # 38 items left
#
setsid wps /media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/08_03_53_Flu_Biosafety/Flu-Biosafety_20210125_Add.docx # Experiment summary from Wang Hui # filename changed # simply revised
#
i=/media/ht/ht_5T/Work/Projects/Biosafety/Ion-e-Air/Drug_Test/20210125
pcmanfm -n ${i}; cd ${i} # revised report and contract for DD
#
i=/media/ht/ht_5T/Work/Projects/Biosafety/甘肃项目/BigData_Project.pptx
setsid wpp ${i} # reviewer's comment added in first page (title page)

SRA Integrity check

You can run our vdb-validate tool. For example:

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vdb-validate --option-file PRJNA_ID_SRR_Acc_List.txt

This will verify the internal checksums for all of the accessions in your accession list file.

You can also validate one at a time. For example:

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vdb-validate SRR000001

You can turn off referential integrity checks if you just want to verify the checksums. It could speed things up. For example:

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vdb-validate -I no --option-file PRJNA_ID_SRR_Acc_List.txt

基于神经网络构建的戊型肝炎病毒时空分布模型的研究

Reading

Macro usage in Linux Office Suite (WPS or LibreOffice)

Expand all items >>

20210123

Contents
  1. 1. Working directories
    1. 1.1. Backup
  2. 2. Joplin - an open source note taking and to-do application with synchronisation capabilities

Working directories

Backup

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# Backup
Source=/media/ht/ht_5T/Work/
Destination=/media/ht/ht_5T_7/Work/
rsync -auP --update ${Source} ${Destination} # 显示过程

Original size

  • 1.2 TiB (1,342,862,000,128 bytes)
  • 1.2 TiB (1,341,994,985,379 bytes)

Joplin - an open source note taking and to-do application with synchronisation capabilities

Expand all items >>

20210122

Contents
  1. 1. Working directories
  2. 2. Legado
  3. 3. 印刷专业词汇集合帖.md
  4. 4. Joplin - an open source note taking and to-do application with synchronisation capabilities

Working directories

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i=/media/ht/ht_5T/Work/DL/20201210
pcmanfm -n ${i}; cd ${i} # organize/clean-up documents  # 45 items left
#
i=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/09_02_63_HEV/CNN/20201209.pptx
setsid wpp ${i} # HEV analysis current status
#
i=/media/ht/ht_5T/Work/肿瘤室工作/0_学生指导/王娇/Thesis
pcmanfm -n ${i}; cd ${i} # 论文撰写开始
#
i=/media/ht/ht_5T/Work/Projects/CC_n_HPV/Alpha_HPV_Project/HPV30_Detect/Ref/Deletion
pcmanfm -n ${i}; cd ${i} # well done

Legado

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i=/media/ht/ht_5T/Management/Legado
pcmanfm -n ${i}; cd ${i} # Description and instruction of Legado
#
i=/media/ht/ht_5T/Management/lHT_Media/Legado.md
subl ${i}

使用备份功能，手机A的备份可以被手机B的恢复功能输入手机A的书目，同时保留原来手机B的原有书目。

印刷专业词汇集合帖.md

Joplin - an open source note taking and to-do application with synchronisation capabilities

Expand all items >>

20210121

Contents
  1. 1. Working directories
  2. 2. How to set “date modified” by “date taken” with Exiftool? - Photography Stack Exchange

Working directories

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hexo new `date +%Y%m%d`
printf "\n\n# Working direcotries\n\n" >> `Date`.md
subl `date +%Y%m%d`.md
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i=/media/ht/ht_5T/Work/Projects/CC_n_HPV/Alpha_HPV_Project/HPV30_Detect/Draft
cd ${i} # moving `.xmind` to there
#
i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Submission/1
cd ${i} # organize documents in schedule
#
i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Submission/1; pcmanfm -n ${i}
#
i=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/08_03_53_Flu_Biosafety; pcmanfm -n ${i}

How to set “date modified” by “date taken” with Exiftool? - Photography Stack Exchange

to be solved

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ExifTool "-FileModifyDate<XMP:DateTimeOriginal" "-FileModifyDate<EXIF:CreateDate" "-FileModifyDate<XMP:CreateDate" "-FileModifyDate<$IPTC:DateCreated $IPTC:TimeCreated" "-FileModifyDate<EXIF:DateTimeOriginal" DIR
#
exiftool '-filemodifydate<datetimeoriginal' -r -if '$datetimeoriginal ne substr($filemodifydate,0,19)' -ext jpg .
#exiftool '-filemodifydate<datetimeoriginal' -r -if '$datetimeoriginal ne substr($filemodifydate,0,19)' -ext mp3 ./

exiftool "-FileModifyDate<XMP:DateTimeOriginal" "-FileModifyDate<EXIF:CreateDate" "-FileModifyDate<XMP:CreateDate" "-FileModifyDate<$IPTC:DateCreated $IPTC:TimeCreated" "-FileModifyDate<EXIF:DateTimeOriginal" ./

exiftool -fileOrder DateTimeOriginal -recurse -extension jpg -ignoreMinorErrors '-FileName<CreateDate' -d %Y-%m-%d%%-.3nc.%%e "$@"

exiftool -fileOrder DateTimeOriginal -recurse -extension mp3 -ignoreMinorErrors '-FileName<CreateDate' -d %Y-%m-%d%%_.1nc.%%e "$@"

Expand all items >>

20210120

Contents
  1. 1. Working directories
  2. 2. Music storage online

Working directories

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i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Submission/1
cd ${i}
#
# Copy /media/ht/ht_5T/Work/Projects/Other_Projects/Coronavirus_Project/Ref/Vaccine/Vaccine_20210117.pdf to Margin Note 3
i=/media/ht/ht_5T/Work/Projects/Other_Projects/Coronavirus_Project/Ref/Vaccine
cd ${i}

Music storage online

Expand all items >>

20210119

Contents
  1. 1. Working directories
  2. 2. OneDrive
  3. 3. FTP access
  4. 4. Calendar from Microsoft Outlook

Working directories

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i=/media/ht/ht_5T/Work/Projects/NFE/Publication/Draft/Submission
cd ${i}
#
i=/media/ht/ht_5T/Work/Projects/CC_n_HPV/Alpha_HPV_Project/HPV30_Detect/Draft
cd ${i}
# Download debian pack of WPS 2019
#
rm wps-office.deb
ln -s wps-office_11.1.0.9604.XA_amd64.deb wps-office.deb
7z l DEB.7z | awk '{print $5}'
7z a DEB.7z wps-office_11.1.0.9505.XA_amd64.deb wps-office_11.1.0.9604.XA_amd64.deb
#
i='/media/ht/ht_5T/Work/Funding/2021_国家自然科学基金'
cd ${i} # Classify documents

OneDrive

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hotliu@msn.com

FTP access

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ftp
>open IP 2121
#
ftp 192.168.1.6 2121
#

To be solved

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# Error message
227 Entering Active Mode.
Expand/Collapse

Calendar from Microsoft Outlook

  • Edit text with Markor in Android platform
  • Switch between Markor and Calendar

Expand all items >>

{% if theme.mermaid.enable %} {% endif %}

tag:

    缺失模块。
    1、请确保node版本大于6.2
    2、在博客根目录（注意不是yilia根目录）执行以下命令：
    npm i hexo-generator-json-content --save

    3、在根目录_config.yml里添加配置： 

      jsonContent:
    meta: false
    pages: false
    posts:
      title: true
      date: true
      path: true
      text: false
      raw: false
      content: false
      slug: false
      updated: false
      comments: false
      link: false
      permalink: false
      excerpt: false
      categories: false
      tags: true

Step by step.