Working directories

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

############################################################### 国家自然科学基金/NFS
# 
i=/media/ht/ht_5T/Work/Funding/2022_国家自然科学基金/Draft/HLA-G; \
cd ${i}
# 
i=/media/ht/ht_5T/Work/Funding/2022_国家自然科学基金/Draft/HLA-G/Draft.doc; \
setsid wps ${i}
# 
i=/media/ht/ht_5T/Work/Funding/2022_国家自然科学基金/Draft/HLA-G/03-2022年面上项目-正文_HLA-G.docx; \
setsid wps ${i}
############################################################### 讯飞输入法
#
sudo gdebi /media/ht/ht_5T/Stored_Softs/Linux_Softs/IME/packages.deepin.com/deepin/pool/non-free/i/iflyime/iflyime_0.9.988_amd64.deb
############################################################### Candida Ref
#
cd /media/ht/ht_5T/Work/Projects/RTI_Project/Candida/Ref
############################################################### to be organized
#
i=/media/ht/ht_5T/Work/Funding/2022_国家自然科学基金/Draft/HLA-G/1; \
cd ${i}; pcmanfm -n ${i}

Bactch rename

1
2
3
4
5
6
7
8
9
10
11
12

###########################################################################
# Bactch rename
#
Space; Space; Remove_cnmark; Remove_cnmark; Space; Space; rename "s/_and_/_n_/g" *.*

rename 's/^/0/' ?_*.*

rename 's/^/00/' ?_*.*; rename 's/^/0/' ??_*.*
rename 's/^/0/' ??_*.*

for i in *.*; do mv ${i} ${i:4:200}; done

讯飞输入法

• 讯飞输入法官网 - 更好用的手机输入法！

Linux

• com.iflytek.iflyime_1.0.6-7_amd64.deb - 蓝奏云

Windows

• https://download.voicecloud.cn/200ime/iFlyIME_Setup_2.1.1712.exe

Encrypt a USB stick

• How to encrypt a USB stick on Linux, Windows or Mac OS
• Homepage SecurStick
• How to Encrypt an External Hard Drive or USB Flash Drive
• How to protect your data by encrypting your USB drives
• How to encrypt a USB Drive on Linux Operating System? | Linux.Tips

miR

1
2
3

* https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC2675692/
* https://www.thoughtco.com/the-differences-between-sirna-and-mirna-375536
* https://www.cell.com/molecular-therapy-family/nucleic-acids/fulltext/S2162-2531(16)30037-3

• Origins and Mechanisms of miRNAs and siRNAs
• The Differences Between siRNA and miRNA
• siRNA Versus miRNA as Therapeutics for Gene Silencing: Molecular Therapy - Nucleic Acids

2010年人口普查数据表

http://www.stats.gov.cn/tjsj/pcsj/rkpc/6rp/indexce.htm

第四次全国经济普查

没有找到数据表

第三次全国农业普查

没有找到数据表

总和生育率

• 2020人口总和生育率_中国人口生育率走势图_世界人口网手机站

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

-Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients: Cell

Highlights

• A large clinico-genomic database to study metastatic patterns across 50 tumor types
• Oncogenic alteration frequency and chromosomal instability are increased in metastases
• Correlations between chromosomal instability and metastatic burden depend on cancer type
• Genomic features associated with metastasis are identified for specific target organs

Summary

Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma, and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high-grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.

arch linux - Config file for LXDE’s PCManFM - Super User

The configuration file is at ~/.config/pcmanfm/LXDE/desktop-items-0.conf.

To change the desktop folder, change the setting folder.

This is how my file looks:

1
2
3
4
5
6
7
8
9
10
11
12
13
14

[*]
wallpaper_mode=crop
wallpaper_common=1
wallpaper=/home/mb/images/simple_shapes.png
desktop_bg=#000000
desktop_fg=#ffffff
desktop_shadow=#000000
desktop_font=Sans 12
folder=/home/mb/superSpecialDir
show_wm_menu=0
sort=mtime;ascending;
show_documents=0
show_trash=1
show_mounts=0

Face extraction

1

sudo apt-get install ipython python-opencv python-scipy python-numpy python-pygame python-setuptools python-pip

• Search · extract face from image
• kb22/Create-Face-Data-from-Images: This project involves using OpenCV’s trained Face Detection Neural Network to detect faces in various images and extract them either as separate images or create boxes around faces.
• ladrift/face-extractor: Extract face from image using face++
• dnmellen/facehugger: Extracts faces from an image

1
2
3
4

* https://github.com/search?q=extract+face+from+image
* https://github.com/kb22/Create-Face-Data-from-Images
* https://github.com/ladrift/face-extractor
* https://github.com/dnmellen/facehugger

Working directories

10 Best Audio Editors For Linux in 2021 (Free & Paid)

• Best Audio Editors For Linux - It’s FOSS

Edit the music files effectively on your Linux system.

Megan LeaveyApril 15, 2020

Audio Editors For Linux

Music is the best painkiller in the world. But at the same time, it is not that easy to create music. It takes a lot of patience to finetune it. Either for professional graders or newbies, you need audio editors to polish your music. If you are a Linux user and you are in the search of the best audio editor software for Linux OS, you are in the correct place. In this article, we have listed for you the best audio editors for Linux.

List of Best Audio Editors For Linux

• Audacity
• LMMS
• Mixxx
• Virtual DJ
• Qtractor
• Ardour
• guitarix
• Ocenaudio
• Hydrogen Drum Machine
• Rosegarden

Audacity

Audacity is inarguably the best audio editor for Linux OS. It is one of the most popular audio editors among the Linux users.

Copy video URL

Copy video URL at current time

Fullscreen

IMA SDK can’t be loaded

Audacity is an open-source cross-platform audio software. With Audacity, you can record live audio, computer playback, edit any music formats like WAV, FLAC, Ogg Vorbis, MP2, MP3, AIFF, and more. The supported sound qualities are 16-bit, 24-bit, and 32-bit. In addition to that, you can add extra plug-ins like LV2, LADSPA, VST, and more. Audacity provides a wide range of keyboard shortcuts so that you won’t need to use your mouse.

Audacity is available for free and it is available for Windows and Mac too.

LMMS

LMMS (Linux Multimedia Studio) is one of the powerful digital audio workstations.

The LMMS has all the basic audio editing features with some advanced editing tools. It has the most user-friendly interface. With LMMS, you can mix sounds, create sounds using VST, built-in compressor and audio presets. It is developed by music professionals, so you will get the real feel of music editing in this software. For music professionals, it has the spectrum analyzer for advanced audio editing.

LMMS is available for free and it consumes only 89.3 MB of your storage.

Mixxx

Mixxx, the name itself tells that the software is dedicated for audio editors alone.

If you want to have some DJ, Mixxx is the best option. It has all the tools that every DJ needs. With the Mixxx, you can perform live mixes in your own creative way. It will let you know the BPM (Beats per minute) and musical key so that you will mix the next track perfectly. Mixx allows you to add multiple audio effects to the tracks. If you want, you can also use the Master Sync to match the BPM automatically. You can also customize the DJ Hardware with the tools you like.

Like Audacity and LMMS, Mixxx is also available for free.

Virtual DJ

Virtual DJ is a feature-rich audio editor for Linux. It is one of the most used audio and video editors in the world.

Virtual DJ is a powerful audio editor as it will provide you with the tools and options that a real DJ box will have. Though being powerful, it is easy to use. It is one of the oldest audio editors and it has a download count of 100 million. Virtual DJ is the best audio editor for Linux when it comes to library management. You can easily search for tracks, create playlists and smart folders with ease. It has AI suggestions too. In the app, you can find a lot of built-in audio and video effects to enhance your music.

It is available for Windows and Mac only. But you can install Wine on your Linux to run this editor. It costs $19 per month.

Qtractor

Qtractor is one of the fewest audio editors that is developed only for Linux OS. Until now, it is available for Linux only.

The audio editor is written in C++ with the Qt framework, hence the name Qtractor. Since it is targeted for Linux only, the navigation and UI are pretty simple to native Linux users. You can add an infinite number of music tracks to a project without any hanging issues. The supported file formats are OGG, MP3, WAV, AIFF, FLAC. If you want more, you can add them via libsndfile. It has a built-in sound mixer, MIDI clip editor, loop recorder, and many more options.

Qtractor is available for free.

Ardour

Ardour is one of the best audio editors for Linux. It gives you a pleasant audio editing experience.

With Ardour, you can get non-linear editing, mix different audio formats together, record from various sources, add unlimited multichannel tracks, and so on. Ardour is suitable for both personal and professional use. Other than the built-in plug-ins you can add plug-ins from any makers. The supported plug-in formats are OS X, VST, and LV2. The audio editor will display the frame-by-frame timeline of an audio file.

Ardour audio editor is available for free.

guitarix

guitarix is a virtual guitar amplifier for your Linux OS. If you are a guitarist, it is the best audio editor for you.

guitarix takes the audio signal from your guitar and processes them within seconds. The obtained signal from the guitar is processed by a main amp and the rack-section. In the rack-section, you can add more than 25 effects to finetune your music. The maximum time taken for processing is not more than 10 seconds. If you want more plug-ins other than the built-in plug-ins, you can add them from the LADSPA and LV2.

Like Ardour, guitarix is available for free.

ocenaudio

ocenaudio is one of the fastest audio recorders and editors for Linux. It will allow you to edit tracks without any complications.

ocenaudio is based on Ocen Framework. It will let you edit as many files as you want. The time-consuming operations like adding effects, exporting tracks, saving files will be done on the background leaving the full screen for you to edit. Advanced features like support for VST, spectrogram, multi-select mode are available on the ocenaudio. It is one of the best audio editors for beginners.

Like most of the audio editors for Linux, it is available for free.

Hydrogen Drum Machine

Hydrogen Drum Machine is a fast and intuitive audio editor for Linux. It has support for a compressed FLAC file.

With the Hydrogen Drum Machine, you can have the privilege to add an unlimited number of patterns and chain those patterns into a new track. You can add up to 192 ticks per pattern, multi-layer support for instruments, sample editor with basic functions, and advanced tab-tempo. Advanced features like JACK, ALSA, OSS audio drivers, export song to MIDI, lilypond, WAV, AIFF, FLAC, and OGG file.

Hydrogen Drum Machine is available for free.

Rosegarden

Rosegarden is yet another audio editor that is available for Linux. It is a basic audio editor.

Rosegarden has features like music notation editing, track mixing, recording, and basic support for digital audio. It is not recommended for professionals as it doesn’t have any advanced features. It is best suited for beginners who experiment with different tools and features. Rosegarden is easy to learn, thanks to the minimal number of tools. If you are eager to learn the basics of audio editing, Rosegarden is the best editor for you.

Rosegarden is available for free.

Tip! Best Text Editor for Ubuntu [Updated List]

Our opinion

These are the best audio editors for Linux OS. Install any one of these audio editors on your Linux and unleash the creative editor in you. If we missed any of your best audio editors for Linux, mention that in the comments section. Follow techowns on Facebook and Twitter to catch our latest articles instantly.

Best Audio Editors For Linux

• Best Audio Editors For Linux - It’s FOSS

Last updated January 16, 2019 By Ankush Das 34 Comments

You’ve got a lot of choices when it comes to audio editors for Linux. No matter whether you are a professional music producer or just learning to create awesome music, the audio editors will always come in handy.

Well, for professional-grade usage, a DAW (Digital Audio Workstation) is always recommended. However, not everyone needs all the functionalities, so you should know about some of the most simple audio editors as well.

In this article, we will talk about a couple of DAWs and basic audio editors which are available as free and open source solutions for Linux and (probably) for other operating systems.

Top Audio Editors for Linux

We will not be focusing on all the functionalities that DAWs offer – but the basic audio editing capabilities. You may still consider this as the list of best DAW for Linux.

Installation instruction: You will find all the mentioned audio editors or DAWs in your AppCenter or Software center. In case, you do not find them listed, please head to their official website for more information.

1. Audacity

Audacity is one of the most basic yet a capable audio editor available for Linux. It is a free and open-source cross-platform tool. A lot of you must be already knowing about it.

It has improved a lot when compared to the time when it started trending. I do recall that I utilized it to “try” making karaokes by removing the voice from an audio file. Well, you can still do it – but it depends.

Features:

It also supports plug-ins that include VST effects. Of course, you should not expect it to support VST Instruments.

• Live audio recording through a microphone or a mixer
• Export/Import capability supporting multiple formats and multiple files at the same time
• Plugin support: LADSPA, LV2, Nyquist, VST and Audio Unit effect plug-ins
• Easy editing with cut, paste, delete and copy functions.
• Spectogram view mode for analyzing frequencies

Visit Website

[irp posts=2017]

2. LMMS

LMMS is a free and open source (cross-platform) digital audio workstation. It includes all the basic audio editing functionalities along with a lot of advanced features.

You can mix sounds, arrange them, or create them using VST instruments. It does support them. Also, it comes baked in with some samples, presets, VST Instruments, and effects to get started. In addition, you also get a spectrum analyzer for some advanced audio editing.

Features:

• Note playback via MIDI
• VST Instrument support
• Native multi-sample support
• Built-in compressor, limiter, delay, reverb, distortion and bass enhancer

Visit Website

3. Ardour

Ardour is yet another free and open source digital audio workstation. If you have an audio interface, Ardour will support it. Of course, you can add unlimited multichannel tracks. The multichannel tracks can also be routed to different mixer tapes for the ease of editing and recording.

You can also import a video to it and edit the audio to export the whole thing. It comes with a lot of built-in plugins and supports VST plugins as well.

Features:

• Non-linear editing
• Vertical window stacking for easy navigation
• Strip silence, push-pull trimming, Rhythm Ferret for transient and note onset-based editing

Visit Website

4. Cecilia

Cecilia is not an ordinary audio editor application. It is meant to be used by sound designers or if you are just in the process of becoming one. It is technically an audio signal processing environment. It lets you create ear-bending sound out of them.

You get in-build modules and plugins for sound effects and synthesis. It is tailored for a specific use – if that is what you were looking for – look no further!

Features:

• Modules to achieve more (UltimateGrainer – A state-of-the-art granulation processing, RandomAccumulator – Variable speed recording accumulator,
  UpDistoRes – Distortion with upsampling and resonant lowpass filter)
• Automatic Saving of modulations

Visit Website

5. Mixxx

If you want to mix and record something while being able to have a virtual DJ tool, Mixxx would be a perfect tool. You get to know the BPM, key, and utilize the master sync feature to match the tempo and beats of a song. Also, do not forget that it is yet another free and open source application for Linux!

It supports custom DJ equipment as well. So, if you have one or a MIDI – you can record your live mixes using this tool.

Features

• Broadcast and record DJ Mixes of your song
• Ability to connect your equipment and perform live
• Key detection and BPM detection

Visit Website

[irp posts=10941]

6. Rosegarden

Rosegarden is yet another impressive audio editor for Linux which is free and open source. It is neither a fully featured DAW nor a basic audio editing tool. It is a mixture of both with some scaled down functionalities.

I wouldn’t recommend this for professionals but if you have a home studio or just want to experiment, this would be one of the best audio editors for Linux to have installed.

Features:

• Music notation editing
• Recording, Mixing, and samples

Visit Website

Wrapping Up

These are some of the best audio editors you could find out there for Linux. No matter whether you need a DAW, a cut-paste editing tool, or a basic mixing/recording audio editor, the above-mentioned tools should help you out.

Did we miss any of your favorite? Let us know about it in the comments below.

Best Audio Editing and Music Making Software for Linux

• Best Audio Editing and Music Making Software for Linux

This article covers a list of music making or audio editing software usable on Linux. Some of these applications allow you to record sound streams through external devices like microphones while others allow you to capture audio from musical instruments connected to your Linux system.

Audacity

Audacity is one of the most widely used sound editing and recording software available for Linux, Windows and macOS. Audacity is completely free and anyone can access its source code repository as it is an open source software. Its main features include audio recording through microphone and other instruments, support for importing sound files, mixing and editing of audio tracks, configurable sample rates, dithering, spectrogram, respamling, built-in and third-party plugins, sequential editing, edit history, sound effects, full support for navigation through keyboard and so on. You can read more about its features, functionality and user interface elements from its manual available here.

Audacity can be installed in latest versions of Ubuntu by executing the command mentioned below:

$ sudo apt install audacity

You can install the Audacity app from package manager in other Linux based distributions or you can download it from its official website.

Ardour

Ardour is a music making and recording software specially designed for engineers who regularly edit and make music. You can also use it for casual sound editing needs. Main features of Ardour include its ability to capture sound streams through microphone and other connected instruments, input monitoring, multi-layer recording mode, multi-channel and multi-layer tracks, edit history, mixing and merging of clips, support for extracting audio from video files, basic video editing tools, routing, monitor controls, official and third-party plugins, dedicated mixer strips, groups, stream panning, automation macros and so on.

Ardour can be installed in latest versions of Ubuntu by executing the command mentioned below:

$ sudo apt install ardour

You can install Ardour app from package manager in other Linux based distributions or you can download it from its official website.

Rosegarden

Rosegarden is an open source audio sequencer, music notation creator and editor, and MIDI sequencer combined into one. It is mainly designed for editing and mixing audio recorded from musical instruments but it also works with other popular digital audio file formats. Using Rosegarden, you can compose, synthesize, arrange, edit and organize audio files and MIDI data.

Rosegarden can be installed in latest versions of Ubuntu by executing the command mentioned below:

$ sudo apt install rosegarden

You can install the Rosegarden app from package manager in other Linux based distributions or you can download it from its official website.

LMMS

LMMS is a cross-platform and open source software mainly used for producing music. You can create new tracks, mix and synthesize sounds, rearrange clips and use layers. Other features of LMMS include support for MIDI keyboards, MIDI controls, multiple export options, beat editor, looping points, automation macros, piano roll, effects mixer, song editor, built-in presets and samples, and so on.

LMMS can be installed in latest versions of Ubuntu by executing the command mentioned below:

$ sudo apt install lmms

You can install LMMS app from package manager in other Linux based distributions or you can download the official “AppImage” file that runs on any distribution from its official website.

Mixxx

Mixxx is an open source and cross-platform DJ software that can be used to create live mixes and remixes. While it doesn’t work like other audio editors listed above, you can use it to record any live mixes created in real time. Its main mixing features include tempo control, support for external instruments, sound effects, support for controlling vinyl records, cue points, beat control, beat looping, pitch manipulation, built-in equalizer and so on.

Mixxx can be installed in latest versions of Ubuntu by executing the command mentioned below:

$ sudo apt install mixxx

You can install Mixxx app from package manager in other Linux based distributions or you can download it from its official website.

Qtractor

Qtractor is an open source music making software programmed in C++ and designed using Qt toolkit. You can use it to create multi-track and multi-channel sequences of MIDI and various other sound files. Other features of Qtractor include support for mixing and editing of audio clips, edit history, drag-and-drop user interface, plugins, looped recording, crossfading tools, audio normalization, pitch and tempo manipulation, support for time-stretching, sample rate manipulation and so on.

Qtractor can be installed in latest versions of Ubuntu by executing the command mentioned below:

$ sudo apt install qtractor

You can install the Qtractor app from package manager in other Linux based distributions or you can download it from its official website.

Hydrogen

Hydrogen is an open source software that can sequence and synthesize emulated drum patterns or real sounds through external instruments. Other features of Hydrogen include multiple layers, chainable patterns of variable lengths, mixing and editing capabilities, tempo and pitch manipulation, visual metronome, time-stretch function, loop support and so on.

Hydrogen can be installed in latest versions of Ubuntu by executing the command mentioned below:

$ sudo apt install hydrogen

You can install the Hydrogen app from package manager in other Linux based distributions or you can download it from its official website.

Helm

Helm is an open source and cross-platform synthesizer that can be used to create digital music. It features multiple oscillators, waveshaping, shelf filters, arpeggiator, sound effects, step sequencer, multiple waveforms, filters and so on.

Helm can be installed in Ubuntu by downloading installable “.deb” packages available here. Once downloaded, run a command in the following format to install the “.deb” package.

$ sudo apt install ./helm_0.9.0_amd64_r.deb

You can follow instructions available here to install Helm in other Linux based distributions.

Conclusion

These are some of the best, free, and open source software that you can use to record, edit, mix, synthesize, and directly make music from scratch using external instruments connected to your Linux system.

Working directories

Primer for HSV-2

1
2

cd /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/RPA/Testing/RPA_HSV-2
cat Primer_Detection.tbl | sed 's/^/>/' | sed 's/\t/\n/' | sed 's/G/g/' > Primer_Detection.fas

Audio Editor

• Best Audio Editing and Music Making Software for Linux
• 10 Best Audio Editors For Linux in 2021 (Free & Paid) - TechOwns
• Best Audio Editors For Linux - It’s FOSS

INSDC

International Nucleotide Sequence Database Collaboration

International Nucleotide Sequence Database Collaboration

• The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.

Untitled

• The INSDC advisory board, the International Advisory Committee, is made up of members of each of the databases’ advisory bodies. The International Advisory Committee published a paper reiterating the importance of depositing data to INSDC.
• Individuals submitting data to the international sequence databases should be aware of INSDC policy.

How to submit data

• For full details of how to submit data to the databases, please select a collaborating partner.
• DDBJ, ENA, GenBank
• The INSDC Feature Table Definition Document is available here.

Working directories

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24

###########################################################################
# HQ
# 
cd /media/ht/ht_5T/Work/Projects/HQ2020/Clinic_Trail
# 
###########################################################################
# 国家自然科学基金/NFS
# 
i=/media/ht/ht_5T/Work/Funding/2022_国家自然科学基金/Draft/HLA-G; \
cd ${i}
# 
i=/media/ht/ht_5T/Work/Funding/2022_国家自然科学基金/Draft/HLA-G/Draft.doc; \
setsid wps ${i}
#
###########################################################################
# ht_T7_1 Backup
# 
Drive=ht_T7_1; \
Backup='Work'; \
Source="/media/ht/ht_5T/${Backup}/"; Destination="/media/ht/${Drive}/${Backup}/"; rsync -au --delete ${Source} ${Destination}
#
Backup='Work'; \
du -sh /media/ht/ht_T7_1/${Backup}/ /media/ht/ht_5T/${Backup}/; du -sk /media/ht/ht_T7_1/${Backup}/ /media/ht/ht_5T/${Backup}/
# 

HPV LCR

• “HPV_Mutation_Raw_Data.pptx”, originally from Li Ying
• Changed to “LCR_Sum.pptx”

1
2

cd /media/ht/ht_5T/Work/Projects/CC_n_HPV/LCR-Binding_Protein/Summary
setsid wps /media/ht/ht_5T/Work/Projects/CC_n_HPV/LCR-Binding_Protein/Summary/LCR_Sum.pptx

Draft

HPV16

1

cd /media/ht/ht_5T/Work/Projects/CC_n_HPV/HPV16_isolate_project

HPV51

1

cd /media/ht/ht_5T/Work/Projects/CC_n_HPV/Alpha_HPV_Project/HPV51_Detect/Draft

ZIM download

• ZIM
• ZIM/wikisource

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67

###########################################################################
# Backup 20220210
# Wed 09 Feb 2022 10:30:39 AM CST
# 
Source=/media/ht/ht_5T/Database/Wikipedia/ZIM/20220205
Target=/media/ht/ht_5T/Database/Wikipedia/ZIM/20220205
pcmanfm -n /media/ht/ht_5T/Database/Wikipedia/ZIM/EN /media/ht/6T_21/Wikipedia/ZIM/DLed
# 
pcmanfm -n /media/ht/ht_5T/Database/Wikipedia/ZIM/EN; pcmanfm -n /media/ht/6T_21/Wikipedia/ZIM/DLed
# 
cd /media/ht/ht_5T/Database/Wikipedia/Kiwix/
cd /media/ht/ht_5T_9/ht_RS/Kiwix
# 
###########################################################################
# 
http://download.kiwix.org/zim/wikinews/wikinews_en_all_maxi_2021-12.zim
http://download.kiwix.org/zim/wikinews/wikinews_en_all_maxi_2022-01.zim
http://download.kiwix.org/zim/wikinews/wikinews_en_all_nopic_2021-12.zim
http://download.kiwix.org/zim/wikinews/wikinews_en_all_nopic_2022-01.zim
# 
axel http://download.kiwix.org/zim/wikinews/wikinews_en_all_maxi_2021-12.zim
axel http://download.kiwix.org/zim/wikinews/wikinews_en_all_maxi_2022-01.zim
axel http://download.kiwix.org/zim/wikinews/wikinews_en_all_nopic_2021-12.zim
axel http://download.kiwix.org/zim/wikinews/wikinews_en_all_nopic_2022-01.zim
###########################################################################
# en
# 
cd /media/ht/ht_5T/Database/Wikipedia/Kiwix/EN
axel http://download.kiwix.org/zim/wikipedia/wikipedia_en_all_maxi_2021-12.zim # Downloaded
###########################################################################
# cn
# 
cd /media/ht/ht_5T/Database/Wikipedia/Kiwix/CN
axel http://download.kiwix.org/zim/wikipedia/wikipedia_zh_all_maxi_2022-01.zim # Downloaded
###########################################################################
# gutenberg
# 
cd /media/ht/ht_5T/Database/Wikipedia/Kiwix/20220205
axel http://download.kiwix.org/zim/gutenberg/gutenberg_en_all_2021-12.zim # Downloaded
# 
cd /media/ht/ht_5T/Database/Wikipedia/Kiwix/20220205
axel http://download.kiwix.org/zim/gutenberg/gutenberg_en_all_2022-01.zim # Downloaded
# 
i='/media/ht/ht_5T/Database/Wikipedia/Kiwix/20220205/gutenberg_en_all_2022-01.zim'
ls -sh ${i}; ls -sk ${i}
###########################################################################
# wikisource
# 
cd /media/ht/6T_21/Wikipedia/ZIM/20220207
i=http://download.kiwix.org/zim/wikisource/wikisource_ja_all_maxi_2022-01.zim
axel ${i} # Downloaded
# 
i=http://download.kiwix.org/zim/wikisource/wikisource_ja_all_maxi_2022-02.zim
axel ${i} # Downloaded
###########################################################################
# /media/ht/6T_21/Wikipedia/ZIM Backup
#
###########################################################################
# wiktionary
#
cd /media/ht/6T_21/Wikipedia/ZIM/20220207
axel http://download.kiwix.org/zim/wiktionary/wiktionary_ja_all_maxi_2022-02.zim # Downloaded
axel http://download.kiwix.org/zim/wiktionary/wiktionary_ja_all_maxi_2022-01.zim # Downloaded
axel http://download.kiwix.org/zim/wiktionary/wiktionary_zh_all_maxi_2022-01.zim # Downloaded
axel http://download.kiwix.org/zim/wiktionary/wiktionary_zh_all_maxi_2021-12.zim # Downloaded
axel http://download.kiwix.org/zim/wiktionary/wiktionary_en_all_maxi_2021-10.zim # Downloaded
axel http://download.kiwix.org/zim/wiktionary/wiktionary_en_all_maxi_2022-01.zim # Downloaded

Kiwix installation

• Ubuntu PPA - Kiwix

1
2
3

sudo add-apt-repository ppa:kiwixteam/release
sudo apt install software-properties-common
sudo apt install kiwix

Working directories

1
2
3
4

cd /media/ht/ht_5T/Work/Projects/Other_Projects/miR_Project/Ref/Wikipedis
# 
i=/media/ht/ht_5T/Work/Projects/Other_Projects/miR_Project/Ref/Wikipedia/miR_Related_Wikipedia.docx; \
setsid wps ${i}

miR references

Github

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22

i='* https://github.com/search?q=microrna
* https://github.com/mhalushka/miRge
* https://github.com/rajewsky-lab/mirdeep2
* https://github.com/bcgsc/mirna
* https://github.com/hangelwen/miR-PREFeR
* https://github.com/nnalpas/microRNA-sequencing'
echo ${i} | sed 's/\*//' | xargs echo | xargs chromium-browser --new-window
# 
echo '* https://github.com/search?q=microrna
> * https://github.com/mhalushka/miRge
> * https://github.com/rajewsky-lab/mirdeep2
> * https://github.com/bcgsc/mirna
> * https://github.com/hangelwen/miR-PREFeR
> * https://github.com/nnalpas/microRNA-sequencing' | sed 's/\*//' | sed 's/>//' | xargs echo | xargs chromium-browser --new-window
# 
echo '* https://github.com/search?q=microrna
* https://github.com/mhalushka/miRge
* https://github.com/rajewsky-lab/mirdeep2
* https://github.com/bcgsc/mirna
* https://github.com/hangelwen/miR-PREFeR
* https://github.com/nnalpas/microRNA-sequencing' | sed 's/\*//' | xargs echo | xargs chromium-browser --new-window

• Search · microrna
• mhalushka/miRge: miRge - microRNA alignment software for small RNA-seq data, now at v2.0
• rajewsky-lab/mirdeep2: Discovering known and novel miRNAs from small RNA sequencing data
• bcgsc/mirna: microRNA profiling pipeline
• hangelwen/miR-PREFeR: microRNA PREdiction From small RNA-seq data
• nnalpas/microRNA-sequencing: Creation of a repository for microRNA-sequencing pipeline

Wikipedia

1
2
3
4
5
6
7
8
9
10

echo '* https://en.wikipedia.org/wiki/Small_interfering_RNA
* https://en.wikipedia.org/wiki/MicroRNA
* https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software
* https://en.wikipedia.org/wiki/MicroRNA_sequencing
* https://en.wikipedia.org/wiki/MicroRNA_and_microRNA_target_database
* https://en.wikipedia.org/wiki/Nucleic_acid_structure_prediction
* https://www.zhihu.com/question/265991876' | sed 's/\*//
' | xargs echo | xargs chromium-browser
# 
setsid chromium-browser --new-window https://en.wikipedia.org/wiki/Small_interfering_RNA https://en.wikipedia.org/wiki/MicroRNA https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software https://en.wikipedia.org/wiki/MicroRNA_sequencing https://en.wikipedia.org/wiki/MicroRNA_and_microRNA_target_database https://en.wikipedia.org/wiki/Nucleic_acid_structure_prediction https://www.zhihu.com/question/265991876

• Small interfering RNA - Wikipedia
• microRNA - Wikipedia
• List of RNA structure prediction software - Wikipedia
• MicroRNA sequencing - Wikipedia
• MicroRNA and microRNA target database - Wikipedia
• Nucleic acid structure prediction - Wikipedia

Small RNA database

• RNAcentral: The non-coding RNA sequence database
• Small RNA Database | Nucleic Acids Research | Oxford Academic
• Frontiers | LuluDB—The Database Created Based on Small RNA, Transcriptome, and Degradome Sequencing Shows the Wide Landscape of Non-coding and Coding RNA in Yellow Lupine (Lupinus luteus L.) Flowers and Pods | Genetics

siR database

• sirna database - Google Search
• siRNAdb: a database of siRNA sequences | Nucleic Acids Research | Oxford Academic
• RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity | Database | Oxford Academic
• siRNAdb: a database of siRNA sequences - PubMed
• HuSiDa–the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells - PubMed

miR and siR

• microrna sirna difference - Google Search
• Origins and Mechanisms of miRNAs and siRNAs
• The Differences Between siRNA and miRNA
• siRNA Versus miRNA as Therapeutics for Gene Silencing: Molecular Therapy - Nucleic Acids

Mark Text

• Mark Text
• marktext/marktext: 📝A simple and elegant markdown editor, available for Linux, macOS and Windows.
• Install Mark Text Markdown Editor On Ubuntu Linux

1
2
3

flatpak install flathub com.github.marktext.marktext
# 
flatpak run com.github.marktext.marktext

11 Best Markdown Editors for Linux

Last updated October 29, 2020 By Munif Tanjim 52 Comments

Markdown is a simple markup language. It’s lightweight and easy to learn. If you haven’t seen any markdown document yet, just head over to GitHub and enter any open-source project. The README file almost certainly will be written using Markdown.

Basically, you use some ‘code’ before your text and your text will be formatted for display accordingly. For example, if you use asterisks (*) before and after the text, it will be displayed in bold text. Not just GitHub, even several social media websites support Markdown, including Facebook.

It’s often useful in writing documents, especially for developers. You can refer to this Markdown cheat sheet for quick reference.

Non-FOSS alert!

Some applications mentioned here are not open source. They are listed here because they are available on Linux and the article’s focus is on Linux.

Best Markdown Editors for Linux

Today we’re going to present a list of what we think are the best Markdown editors for Linux. Just for clarification, the list is not in any specific order.

If you do not want to install a software, you may check the list of online markdown editors.

Please note that this is not a ranking list.

1. Remarkable

Remarkable has been around for years. It has a minimal and simple user interface. The main points of Remarkable are:

• Interface: Dual pane (Source & Preview)
• Extra Markdown features: Footnotes, superscript, subscript, abbreviations etc. (Pandoc‘s syntax)
• GitHub flavored Markdown: Yes
• Code Syntax Highlighting: Yes
• Export to: HTML & PDF
• Math Blocks: MathJax support
• Customizable: Styling via CSS
• Misc: Plugins & extensions

Remarkable is under active development at the GitHub Project Page. It is worth noting that it is absolutely lightweight.

Install Remarkable on Linux

You can easily grab the DEB file from the Remarkable download page and install it on any Debian-based distro. In case you didn’t know, you can explore different ways to install a DEB files.

Installing using the deb file in Ubuntu 20.04 will give you an error because of dependency issues, but it should work in 19.10 or lower. You can also find it in AUR if you’re using an Arch-based Linux distribution.

Remarkable

2. GitBook

GitBook is a  modern open-source and simple online solution to documentation, digital writing and publishing. And their editor fully supports markdown format.

• Interface: Full fledged document processor
• GitHub flavored Markdown: Yes
• Code Syntax Highlighting: Yes
• Export to: HTML, PDF, ePub, MOBI etc.
• Math Blocks: Yes
• Customizable: Extensive customization options
• Misc: Git integration, Plugins

It is worth noting that it is an online-only editor which was previously available as a standalone app for Linux. So, you’d need to use your browser to make use of it.

If you need a feature-rich document processor that supports markdown, can keep track of document history or want to write a book using markdown document, GitBook is definitely for you!

GitBook

3. Abricotine

Abricotine is an open-source markdown editor based on modern web technology. The main features of Abricotine:

• Interface: Single pane with live preview
• GitHub flavored Markdown: Yes
• Code Syntax Highlighting: Yes
• Export to: HTML
• Math Blocks: LateX
• Customizable: Templates
• Misc: Table of content in side pane

It’s simple and easy to use. Also, you get a live preview of the markdown text in the same window to make things easier.

Install Abricotine on Linux

For Debian-based distros, you can get the DEB file from its GitHub releases section and install it.

If you’re running any other Linux distro or Windows/Mac, you might want to check the official installation instructions.

Abricotine

4. ghostwriter

ghostwriter is a simple, distraction-free editor for markdown. Let’s see what it offers:

• Interface: Single pane
• GitHub flavored Markdown: Yes
• Code Syntax Highlighting: No
• Export to: HTML (& more by dependencies)
• Math Blocks: No
• Customizable: Themes, Styles
• Misc: Focus & Hemingway Mode, Cheat sheet

ghostwriter had a theme repository on GitHub if you want to explore making a custom theme for yourself. It also offers in-built themes.

If you want a dead simple, minimal and robust markdown editor without any fancy features, ghostwriter is really a good choice.

Install ghostwriter on Linux

You can either utilize the Flatpak package available for any Linux distro or add the PPA to install it on a Debian-based distro using the following command:

1
2
3

sudo add-apt-repository ppa:wereturtle/ppa
sudo apt update
sudo apt install ghostwriter

If you didn’t know about Flatpak, I’d suggest you to check out our Flatpak guide. In either case, you can refer to its GitHub releases page to explore options to install it on other Linux distros.

ghostwriter

Recommended Read:

Boostnote: Open Source Note Taking App For Programmers

Organize your quick notes and code snippets in segregated folders with this open source note taking app for programmers.

5. Apostrophe

Apostrophe is a fork of UberWriter by the original developers (kind of a re-brand). It aims to be a distraction-free Markdown editor.

It uses pandoc for markdown while offering a clean and intuitive user experience. You can opt to get live-preview by enabling the half-width view and explore other options as needed.

Install Apostrophe on Linux

It provides a Flatpak package if you prefer using it on any Linux distribution. You can find it in AUR for Arch Linux and Fedora’s official repository to directly install it from the terminal.

For more information on it, you can head to their GitLab page.

Apostrophe

6. ReText

ReText is a simple open-source text editor for markup languages like Markdown and reStructuredText. Let’s have a look at ReText features:

• Interface: Single or Dual pane
• GitHub flavored Markdown: No
• Code Syntax Highlighting: No
• Export to: HTML, ODT, PDF
• Math Blocks: Yes (MathJax/online)
• Customizable: Color scheme
• Misc: Export extensions & Markdown extensions

If you’re working with reStructuredText and looking for a simple editor that also supports Markdown, this could be a great pick.

Install ReText on Linux

On Debian-based distros, you should be able to find it in the Software Center. Or, you can also install it through the terminal by typing:

1

sudo apt install retext

You can explore other options on its GitHub page for different Linux distros.

ReText

7. Mark My Words

Mark My Words is a minimal markdown editor. Here are features that you’ll find:

• Interface: Dual pane
• GitHub flavored Markdown: No
• Code Syntax Highlighting: No
• Export to: HTML & PDF
• Math Blocks: No

It is an interesting open-source markdown editor that’s simple to use while offering the essential features.

Install Mark My Words on Linux

It does not support Ubuntu 20.04 yet (at the time of updating this article). However, you can try it on Ubuntu 19.10 or lower by typing in the following commands in your terminal:

1
2
3

sudo add-apt-repository ppa:voldyman/markmywords
sudo apt update
sudo apt install mark-my-words

There’s also a package available for openSUSE, but you would need to explore its GitHub page to explore more about it.

Mark my Words

8. Scrivenvar

Scrivenvar is an interesting Java-based markdown editor that supports live preview and string interpolation as well.

The user interface is easy to use as well. As far as my initial impressions go, it features all the essential features of a markdown editor. User-defined string interpolation and real-time live preview are two of key highlights here.

Install Scrinvenvar on Linux

It offers an executable binary file on its GitHub page. You just have to download it, navigate to path where you store it, make it executable, and run it.

As an example, I have it on my Downloads directory, here’s what I need to type:

1
2
3

cd Downloads
chmod +x scrivenvar.bin
./scrivenvar.bin

You can explore more about it for other platforms (Windows/Mac) on its GitHub page.

Scrivenvar

9. Typora (Not FOSS)

When it comes to markdown editors, Typora is as simple and elegant as it gets. It’s one of the most polished and feature-rich markdown editors we have encountered.

Let’s take a look at what Typora offers:

• Interface: Single pane seamless preview with live rendering support
• Extra Markdown features: Table of Content, Diagrams
• GitHub flavored Markdown: Yes
• Code Syntax Highlighting: Yes
• Export to: HTML, PDF, ePub, Word, OpenOffice and a bunch of other formats.
• Math Blocks: Tex/LaTex support
• Customizable: Themes
• Misc: Typewriter, Focus and Source Code Modes.

Typora also offers a Themes Gallery and detailed Support Documentation.

The only drawback Typora has is that it isn’t open source and according to their official website, it’s free only during the beta version. So, when the stable build will be released you may have to pay for it.

Install Typora on Linux

You can download the binary file (archived package) from the official website or enter the following commands to add the repository and install it on Ubuntu:

1
2
3
4

wget -qO - https://typora.io/linux/public-key.asc | sudo apt-key add -
sudo add-apt-repository 'deb https://typora.io/linux ./'
sudo apt update
sudo apt install typora

Typora

10. Caret (Not FOSS)

Caret is a premium markdown editor with minimal interface and a bunch of robust markdown features. Let’s take a look at those:

• Interface: Single or Dual pane
• Extra Markdown features: Table of contents, footnotes etc.
• GitHub flavored Markdown: Yes
• Code Syntax Highlighting: Yes
• Export to: PDF
• Math Blocks: Yes
• Customizable: Theme
• Misc: Dark, Focus & Typewriter Modes, Auto-completion etc.

The high cost (about $29 for a license) can be a deal breaker for Linux users looking for FOSS solutions. Otherwise, it’s a great markdown editor.

Install Caret on Linux

You can find both DEB and RPM packages in their GitHub releases section. You just have to download them and install. Even though the latest releases are labelled as beta versions, it still works well.

Caret

11. WordMark (Not FOSS)

WordMark is a lightweight markdown editor with publishing tools for online platforms. WordMark offers the followings:

• Interface: Single or Dual pane with optional sidebar
• GitHub flavored Markdown: Yes
• Code Syntax Highlighting: Yes
• Math Blocks: Yes
• Customizable: Appearance
• Misc: Focus & Vim Modes, Publish to various online platforms

Even though it’s not an open-source solution, it works pretty well on Linux and it’s something worth a try.

Install WordMark on Linux

At the time of updating this article, WordMark offered only a DEB package in its GitHub release section. So, if you’re using any other Linux distro except Debian-based options, you may have to explore its official website to find solutions (if there’s any)

WorkMark

Recommended Read:

Best Free Online Markdown Editors That Are Also Open Source

No need to install. Use these free online markdown editors to write and save your markdown notes. Some editors also offer real-time collaboration.

Honorable Mentions

1. Haroopad (Discontinued)

2. LightMd Editor (Discontinued)

3. EME (Discontinued)

4. PileMd (Discontinued)

Wrapping Up

While there are a lot of markdown editors out there. Here, we tried to list the best of them.

Which one do you consider the best Markdown editors for Linux? Did we miss your favorite Markdown editor? Let us know your thoughts in the comments below.

Working directories

RPA probe

• p96 in summarized PDF document

1

# p1489 B2

Order forms

1
2

i='/media/ht/ht_5T/Work/References/Manufacturer_Manual/TwistDx/Handbooks/Oligo_Order'; \
cd ${i}

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24

├── Basic_oligonucleotide_forms
│   ├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5.xls
│   ├── 2_eurogentec-oligo-batch-order-v8-7-twistamp.xlsx
│   └── Basic_oligonucleotide_forms.7z
├── exo_oligonucleotide_forms
│   ├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5-1.xls
│   ├── 2_eurogentec-oligo-batch-order-v8-7-twistamp-2.xlsx
│   ├── 3_twistamp_exo_order_form_biosearch.xls
│   ├── 4_twistamp_exo_order_form_generic.xls
│   └── exo_oligonucleotide_forms.7z
├── fpg_oligonucleotide_forms
│   ├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5.xls
│   ├── 2_eurogentec-oligo-batch-order-v8-7-twistamp.xlsx
│   ├── 3_twistamp_fpg_order_form_biosearch.xls
│   ├── 4_twistamp_fpg_order_form_generic.xls
│   └── fpg_oligonucleotide_forms.7z
└── nfo_oligonucleotide_forms
    ├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5-1.xls
    ├── 2_eurogentec-oligo-batch-order-v8-7-twistamp.xlsx
    ├── 3_twistamp_nfo_order_form_biosearch.xls
    ├── 4_twistamp_nfo_order_form_generic.xls
    └── nfo_oligonucleotide_forms.7z

4 directories, 18 files

├── Basic_oligonucleotide_forms
│   ├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5.xls
│   ├── 2_eurogentec-oligo-batch-order-v8-7-twistamp.xlsx
│   └── Basic_oligonucleotide_forms.7z
├── exo_oligonucleotide_forms
│   ├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5-1.xls
│   ├── 2_eurogentec-oligo-batch-order-v8-7-twistamp-2.xlsx
│   ├── 3_twistamp_exo_order_form_biosearch.xls
│   ├── 4_twistamp_exo_order_form_generic.xls
│   └── exo_oligonucleotide_forms.7z
├── fpg_oligonucleotide_forms
│   ├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5.xls
│   ├── 2_eurogentec-oligo-batch-order-v8-7-twistamp.xlsx
│   ├── 3_twistamp_fpg_order_form_biosearch.xls
│   ├── 4_twistamp_fpg_order_form_generic.xls
│   └── fpg_oligonucleotide_forms.7z
└── nfo_oligonucleotide_forms
├── 1_btioligoorder8f2d67a1f42264a8875eff0000c536f5-1.xls
├── 2_eurogentec-oligo-batch-order-v8-7-twistamp.xlsx
├── 3_twistamp_nfo_order_form_biosearch.xls
├── 4_twistamp_nfo_order_form_generic.xls
└── nfo_oligonucleotide_forms.7z

奇葩的批量转换

• command line - Converting multiple image files from JPEG to PDF format - Unix & Linux Stack Exchange
• command line - Convert a directory of JPEG files to a single PDF document - Ask Ubuntu

以上两个链接中，真有神奇的命令。

1
2
3

convert *.jpg -auto-orient pictures.pdf
# 
convert *.jpg +adjoin page-%d.pdf

下面的更牛！居然可以OCR。

1. Make PDF

   img2pdf *.jp* --output combined.pdf

2. (optional) OCR the output PDF

   ocrmypdf combined.pdf combined_ocr.pdf

又知道一个新的软件

1

pdfjam --a4paper *.jpg

下面的Shell命令组合，让人神往

1

parallel convert '{} {.}.pdf' ::: *.jpg

A tiny script would do the trick. (tested with ksh88 on Solaris 10)

script.ksh

1
2
3
4
5
6

#!/bin/ksh

[[ $# != 1 ]] && exit 255 # test for nr of args

pdfname=$(sed -e 's/\(.*\)\.jpg/\1\.pdf/' <(echo $"1")) #replace *.jpg with *.pdf
convert "$1" $pdfname

Then you can run find to execute the script:

1

find dir -name image\*.jpg -exec /bin/ksh script.ksh {} \;

引物整理

1

cd /media/ht/ht_5T/Work/肿瘤室工作/日常管理/引物管理

miRDeep2, miR Prediction

1

cd /media/ht/ht_5T/Database/miR_Base/miR_Prediction/miRDeep2/Installation

Working directories

• Great! Worked on Vision.

miR in HSV-1 exosomes

Goal

• 外泌体包含miR的功能
• 选择病毒感染形成外泌体中包含的miR并分析其功能
• 分别讨论宿主端和病毒端miR的功能

Host side

1. Clean.fa中排除HSV-1序列，获得宿主侧序列集合(Host set)
2. 宿主侧序列集合(Host set)中排除miR序列，获得宿主侧非 miR序列集合(Host set miR free)
3. 宿主侧序列集合中miR序列确认，获得宿主侧非miR序列集合(Host miR set)
4. 宿主侧非 miR序列集合(Host set miR free)以及宿主侧非miR序列集合(Host miR set)比较分析，即，HSV-1感染条件下与非感染条件下的数据比较

Virus side

1. Clean.fa中包含与HSV-1一致的序列，获得病毒侧序列集合(Viral set)
2. 病毒侧序列集合(Viral set)中排除miR序列，获得病毒侧非 miR序列集合(Viral set miR free)，该集合中应该存在新的HSV-1编码的miR
3. 病毒侧序列集合(Viral set)中保有miR序列，获得病毒侧非miR序列集合(Viral miR set)
4. 按照前述宿主侧序列的比较方式进行分析

RStudio installation

Working directories

1
2
3
4
5
6
7
8

E: Failed to fetch http://cn.archive.ubuntu.com/ubuntu/pool/universe/f/fonts-wqy-zenhei/fonts-wqy-zenhei_0.9.45-7ubuntu1_all.deb  Connection failed [IP: 91.189.91.39 80]
E: Failed to fetch http://cn.archive.ubuntu.com/ubuntu/pool/universe/f/fonts-wqy-microhei/fonts-wqy-microhei_0.2.0-beta-3_all.deb  Connection failed [IP: 91.189.91.39 80]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
# 
#########################################################################
# knitr powerpoint
cd /media/ht/ht_5T/Work/Conferences/Template

miRDB

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40

cd /media/ht/ht_5T/Database/miR_Base/miRDB
wget http://mirdb.org/download/miRDB_v6.0_prediction_result.txt.gz
wget http://mirdb.org/download/miRDB_v5.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v4.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v3.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v2.0_prediction_result.txt.gz
wget http://mirdb.org/download/MirTarget2_v1.0_prediction_result.txt.gz

# 
lh `locate -b NC_001806_HSV-1.fas`
locate -b NC_001806_HSV-1.fas
# 
i=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/NC_001806_HSV-1.fas
j=/media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20211117/LNG1/Original/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
j=/media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20211117/LNG2/Original/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
j=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/20191025_1255/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
j=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/20191025/NC_001806_HSV-1.fas
rm ${j}; ln -s ${i} ${j}
# 
cd /media/ht/ht_5T/Work/Projects/Exosome/RNA-Seq/20211203/Analysis/20220109

DB=/media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/MagicBLAST/HSV1_Ref
Query=/media/ht/ht_5T/Work/Projects/Exosome/RNA-Seq/20211203/Clean_Ctrl.fa
# 
Ref=
Seq=
Seq_Base=`basename ${Seq}`; Ref_Base=`basename ${Ref%.*}`; BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`.bam
magicblast -query ${Seq} -subject ${Ref} -infmt fasta -outfmt sam | samtools view -bS -F 4 -> ${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam # 序列中绝对禁止`-`，这类符号是经过MSA产生的
BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam
samtools sort $BAM > "${BAM%.bam}.sort.bam"
samtools index "${BAM%.bam}.sort.bam"


Query=/media/ht/ht_5T/Work/Projects/Exosome/RNA-Seq/20211203/Clean_HSV1.fa

samtools

• Sambamba: process your BAM data faster!

wkhtmltopdf

• wkhtmltopdf

1
2

i=https://wkhtmltopdf.org/
wkhtmltopdf ${i} `basename ${i}`.pdf

Working directories

1
2
3

# http://ugene.net/download.html
cd /media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/UGENE/Installer/1
axel https://github.com/ugeneunipro/ugene/releases/download/41.0/ugene-41.0-linux-x86-64.tar.gz

Working directories

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26

cd /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/RPA/Ref/1
# 
sudo npm install -g cnpm --registry=https://registry.npm.taobao.org
#
cd /media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20211123/RPA/Primer_Design_20211124/Confirm
i=
cat ${i} | awk '{print ">"$1 "_F\t"$5}' | sed 's/\t/\n/' > ${i%.*}_L.fas; cat ${i} | awk '{print ">"$1 "_R\t"$6}' | sed 's/\t/\n/' > ${i%.*}_R.fas; cat ${i%.*}_L.fas ${i%.*}_R.fas > ${i%.*}_All.fas
# 
cd /media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20211123/RPA/Primer_Design_20211124/Confirm
# 
BLASTn /media/ht/ht_5T/Database/Virus/Coronavirus/Variants/SARS-CoV-2_VOI_VOC_Sum_20211124.fasta Primer_Output_20211124_Sum_All_Trim.fas
primerBLAST /media/ht/ht_5T/Database/Virus/Coronavirus/Variants/SARS-CoV-2_VOI_VOC_Sum_20211124.fasta Primer_Output_20211124_Sum_All_Trim.fas
# 
i='/media/ht/ht_5T/Database/Virus/Coronavirus/Variants/SARS-CoV-2_VOI_VOC_Sum_20211124.fasta'
j='Primer_Output_20211124_Sum_All_Trim.fas'
BLASTn ${i} ${j}
primerBLAST ${i} ${j}
# 
i='/media/ht/ht_5T/Database/Virus/Coronavirus/SARS-CoV-2_NC_045512.fasta'
j='Primer_Output_20211124_Sum_All_Trim.fas'
BLASTn ${i} ${j}
primerBLAST ${i} ${j}
# 
/media/ht/ht_5T_10/eBooks/History/四库全书/Git/1/KR4/KR4d0445_松雪斋集元赵孟__.txt
/media/ht/ht_5T_10/eBooks/History/四库全书/Git/1/KR5/KR5a0164_玄元十子图赵孟__.txt

URL

https://www.nobelprize.org/prizes/lists/all-nobel-laureates-in-physiology-or-medicine/

• NobelPrize.org

Release Release v2.0.3 · Zettlr/Zettlr

讯飞输入法

• Index of /deepin/pool/non-free/i/iflyime/

1

[iflyime_0.9.85_amd64.deb](http://packages.deepin.com/deepin/pool/non-free/i/iflyime/iflyime_0.9.85_amd64.deb) 11-Apr-2020 05:54 50238044

Primer Design

Primer Design

• Exercises on primer design - BITS wiki

QPCR analysis using qbasePLUS

Sublime Text 4 Build 4113 Crack With Full License Key 2020 [Latest]

• Linux Package Manager Repositories – Sublime Text Documentation

The apt repository contains packages for both x86-64 and arm64.

Install the GPG key:

1

wget -qO - https://download.sublimetext.com/sublimehq-pub.gpg | sudo apt-key add -

Ensure apt is set up to work with https sources:

1

sudo apt-get install apt-transport-https

Select the channel to use:

Stable

1

echo "deb https://download.sublimetext.com/ apt/stable/" | sudo tee /etc/apt/sources.list.d/sublime-text.list

Dev

1

echo "deb https://download.sublimetext.com/ apt/dev/" | sudo tee /etc/apt/sources.list.d/sublime-text.list

Update apt sources and install Sublime Text

1
2

sudo apt-get update
sudo apt-get install sublime-text

Procedures of agarose gel making

1. 制胶器包含3种部件：白色底板、制胶槽和梳子。这样便于下面的描述。
2. 使用200ml三角瓶，称量0.64g(配制0.8%琼脂糖胶)，加入80ml的0.5 x TBE，混匀后在三角瓶口敷以保鲜膜(Saran wrap)，并用牙签扎3个孔。置于微波炉，设置功率800W，约1分钟后观察是否沸腾，后，每次增加10秒，直至沸腾。然后，每次增加10秒加热，观察到至少5次再次沸腾。
3. 至少放置熔化的琼脂糖胶5分钟，这期间执行对制胶器的清洁。
4. 仅使用最大的制胶器以及25孔的梳子。推荐使用3个梳子，最少使用2个梳子。
5. 使用酒精向制胶器所有部件喷洒，特别是将要使用的梳子的部分、制胶槽的上下两面以及白色底板上与制胶槽接触的内面。然后，使用干纸仔细擦拭酒精喷洒的部位，一边擦拭一边对着光线观察擦拭表面是否残留的杂质。
6. 清洁后，安装白色底板和制胶槽，观察两者间是否有空气。梳子放在一边备用。
7. 向熔化的琼脂糖胶中加入4micro-l的EtBr，保证没有产生气泡的情况下混匀。
8. 将上述琼脂糖胶加入安装好的没有梳子的制胶器后，使用牙签轻按制胶槽底部，设法驱赶在白色底板和制胶槽之间形成的气泡。然后，使用牙签驱赶琼脂糖胶表面可能形成的气泡。
9. 小心放置梳子。
10. 至少20分钟的静置。
11. 为保证最高质量，制胶后30分钟内使用。剩余的琼脂糖胶，使用保鲜膜包裹，避光保存与4C冰箱。科室内曾经向王恩龙专门订购过琼脂糖胶保存盒。