Larkum Lab - User contributions [en]

Using GIN

2021-03-26T12:04:34Z

Seharake: draft

You need to use the terminal emulator to use Gin offline.

There is the [https://gin.g-node.org web interface for Gin] that can be used to manage repositories online, but with some limitations (only up to 100 files with <1GB/file can be uploaded).

== Installation ==

https://gin.g-node.org/achilleas/gin-cli-builds/

=== Windows ===

# Download the version 1.12dev ZIP file (either "gin-cli-1.12dev-windows32.zip" or "gin-cli-1.12dev-windows64.zip", depending on your CPU architecture).
# Inspect the archive, and move the content of the archive to e.g. "C:\Programs\Gin".
# Double-click "C:\Programs\Gin\set-global.bat".

Now open your terminal emulator. Running "where gin" should show the path, e.g. "C:\Programs\Gin\gin.bat".

=== MacOS ===

# Download the "gin-cli-latest-macos.zip" and double click the downloaded file to extract the contents.
# Place the extracted contents under e.g. "/Users/<your name>/Gin". You will see the program file with the path "/Users/<your name>/Gin/gin".
# Add the parent directory (e.g. "/Users/<your name>/Gin") to PATH.

Now open your terminal emulator. Running "which gin" should show the path to the program file, e.g. "/Users/<your name>/Gin/gin".

=== Linux ===

Only Debian-based distributions (Raspberry Pi OS, Ubuntu, Linux Mint etc.) are supported.

# Download "gin-cli-latest.deb", and double click the ".deb" file.

Now open your terminal emulator. Running "which gin" should show the path to the gin program, e.g. "/usr/local/bin/gin".

== Making gin command-line client available for you ==

# Make sure that you have a Gin account online at https://gin.g-node.org
# Open your terminal emulator in your computer, and run `gin login`. It will ask you your login details (it will happen only once). After it says "successfully logged in", you can manage your repositories that you see online.

== Preparation of a local repository ==

=== Creating a repository online ===

The simplest way of creating a new repository is to do it online, using the web interface.

After logging in, click on the "+" button appearing at the top-right of the page.

- "New repository"
- "Import repository"

== Management of a repository ==

=== (Not recommended) the simplest way ===

Although the "simplest" way of using gin is as follows, it often results in a weird behavior which can ruin your repository very easily. So this way of using gin is not recommended...

- Checking in all the changes you have made so far: `gin commit`
- Reflecting your changes in the on-line copy: `gin upload`
- Locally reflecting the changes made in other computers: `gin download`

Data management basics

2021-03-18T03:26:16Z

Seharake: draft

== Principles ==

# '''Back up as much as possible.'''
# '''Separate code and data''': there are several [[Template repositories for GIN]].
# '''Keep track of everything you did as much as possible''': I recommend the use of version-control systems, including [[Using GIN|GIN]].
# '''Cite the source in terms of the URL''': it is related to [[Publishing your data]].

More info may be found in [[Organizing your code and data]].

== Terminology ==

=== Metadata ===

"Metadata" refers to:

# the parameters you controlled during the experiments to obtain your raw data, as well as
# the uncontrolled parameters during the experiments that you think may have affected your raw data.

=== Raw data ===

"Raw data" is what you get through observation / acquisition after controlling various conditions.

=== Derived data ===

"Derived data" is any other types of data you would obtain by processing the raw data and the metadata.

=== Notes ===

The distinction between raw vs derived data ''may'' be related to the file formats, but it is ''NOT'' determined by its file format. For example, your electrophysiology acquisition may always result in a set of ".ibw" files, but the ".ibw" files that you generate as the result of processing (e.g. the I-V curves) are considered to be derived data.

== In which file format can I use to store my data? ==

=== "Ideal" options ===

Most open-data advocates would encourage you to use a certain "open" format (normally referring to those that are openly maintained by community, instead of being maintained as proprietary assets by a company). These formats include:

* ".txt" files (raw text)
* ".md", ".adoc", ".rst", or ".htm" files (raw text-based, formatted documents; Markdown, AsciiDoc, ReStructuredText or HTML)
* ".csv" or ".tsv" files (raw text-based tables; comma-separated (CSV) or tab-separated (TSV))
* ".png", ".jpg", or ".tif" files (open image formats)
* ".xml", ".json", or ".yaml" files (structured data formats)
* ".h5" files (HDF5-archived data)

=== Practical options ===

What if the data you have is not among the formats listed above (which is most likely)? Don't worry. In most cases, there have already been community efforts to read those types of data on different platforms without paying anything for a certain expensive software. As long as it can be read (i) without paying anything and (ii) without having to use a certain OS (Windows/UNIX), I would say these data files are practically "open".

For example:

* Using free libraries in Python, you can open:
** Matlab data files (with ".mat" extension) with the use of [https://www.scipy.org/ scipy].
** Igor Pro wave files (with ".ibw" extension), Spike2 binary files (with ".smr" extension) and lot more (Axon, Blackrock, Plexon, Intan etc.) by using [https://neo.readthedocs.io/en/stable/ neo].
* [https://fiji.sc/ Fiji] or [https://imagej.net/ ImageJ] can open image files of various formats, including those specific to a certain microscopes (Zeiss, Olympus etc.).
* [https://www.videolan.org/ VLC] can open video files of various formats.

If your format is not listed above, you can always Google it.

=== Unrecommended options ===

Unfortunately, there are always some formats that cannot be opened without paying some extra money, or you have to use a certain platform (often Windows-specific). For example:

* The ".fig" and compiled binary files of Matlab
* The ".smrx" compressed binary files of Spike2
* Videos encoded using the Matrox Imaging Library (MIL)

There is a difficulty with telling what to do with these files because in many cases there are no other options. Also how to define the raw data is always the matter of discussion (for example, could we consider it to be "raw data" if the original data was modified into another format?). But my recommendation is:

* '''It is better backing them up and storing them safely than doing nothing with them'''.
* '''Try to export your data to another, more "open" format''' if you don't mind:
** For Spike2 data files, exporting to ".smr" files will gain much more portability.
** For MIL video files, you have an option of exporting them to the H.264 video files (e.g. by using ZR View).

== Use of version-control systems ==

I encourage you to use a version-control system (VCS) to manage your project because it can help you throughout the process of data management:

# A VCS helps you keep track of your project while keeping your desktop clean.
# At the same time, a VCS can serve as a cloud back-up storage.
# A VCS (and its cloud/online counterpart) helps you share your data and results with others (in many cases, it also comes with the option of data publication).

I recommend [[Using GIN|the use of GIN, with some precautions]].

=== Problems that a VCS can solve ===

TODO

=== Core concepts ===

TODO

Main Page

2021-03-10T23:45:47Z

Seharake: add data management section (nothing more)

== General ==

* [[Onboarding]]
* [[PRIVATE:Using the lab together|Using the lab together]]
* [[PRIVATE:Biosafety|Biosafety]]
* [[How to edit this wiki site]]

== Animals ==
People who are new to animal experiments here, please first refer to [[PRIVATE:Animal protocols|Animal protocols]] page (not yet prepared well).

* [[PRIVATE:Animal protocols|Animal protocols]]
* [[PRIVATE:Animal experiments basics|Animal experiments basics]]
* [[PRIVATE:Ordering animals|Ordering animals]]
* [[PRIVATE:Using animals|Using animals]]
* [[PRIVATE:Using drugs on animals|Using drugs on animals]]
* [[Animals|Notes]]

== Material orders ==

* [[Orders workflow]]

== Experiments ==

* [[Make friends with transgenes]]
* [[Experiments]]

== Data Management ==

* [[Data management basics]]

Make friends with transgenes

2021-03-10T09:55:09Z

Seharake: migrate from another page

== How to introduce transgenes into an organism ==

=== AAV versus Lentiviruses ===

AAV is commonly used in optogenetics experiments. These viruses are preferred over lentiviruses because they remain primarily episomal, while lentiviruses integrate into the genome. This is important because local chromatin structure at the site of genome integration can affect the expression of transgenes, as well as the expression of neighboring genes. The short coding sequences of channelrhodopsins, halorhodopsins, and other optogenetic genes enables them to be packaged in AAVs. Different serotypes of AAVs have also different cell/tissue specificity.

Lentiviruses carrying transgenes integrate into the genome upon infection, and so permit stable expression in both dividing and non-dividing cells.

=== Transgenesis ===

TODO

== Elements of a transgene ==

=== Promoters ===

* '''Non-specific promoters''': CMV (cytomegalovirus ): high transcription rate. The CAG (CMV-Actin-Globin) promoter is one of its derivatives that can have a higher expression rate.

* '''Syn (Synapsis I)''': Neuron specific (excitatory and inhibitory)

* '''CAMKII''' (calcium/calmodulin-dependent protein kinase II): excitatory-specific

Other types of promoters (e.g. PV, Sim-1, ChAT) are commonly used to restrict the expression of the gene to a certain set of cell populations. They are created / used either via:

* carefully dissecting out the genome to look for the region region responsible for population-specific expression (e.g. PV, Syn, CamKII)
* targeted introduction of Cre (or EGFP) gene into an artificial chromosome (BAC), normally followed by a careful examination of proper expression (e.g. ChAT, TH).
* randomly introducing the Cre or EGFP gene into an artificial chromosome (BAC), and then showing to display population specificity of expression. The promoter is named after the gene that was located around the site of Cre/EGFP insertion (e.g. Sim-1, Tlx-5).

Note that the expression pattern of the downstream gene(s) '''does not necessarily correspond to the endogenous expression pattern of that gene'''.

=== Other elements ===

'''WPRE''': Woodchuck Hepatitis Virus (WHP) Post-transcriptional Regulatory Element (WPRE) is a DNA sequence that, when transcribed creates a tertiary structure enhancing expression. Commonly used in molecular biology to increase expression of genes delivered by viral vectors.

'''Flex (or “flip-excision”) switches''' were designed as a genetic tool for researchers to conditionally manipulate gene expression in vivo using site-specific recombination (e.g. Cre).

* DiO (Double-floxed inverse Orientation): "Cre-On" meaning that your gene of interest starts in the inverse/antisense "off" position and is flipped to the sense (on) orientation in the presence of Cre.
* DO (Double-floxed Orientation): A"Cre-off" i.e. your gene of interest starts in the sense orientation and Cre is used to flip it to "off".

== Miscellaneous information ==

* Lines for in vivo spine imaging: B6.Cg-Tg(Thy1-YFP)16Jrs/J (https://www.jax.org/strain/003709).

2021-03-10T03:22:02Z

Seharake: /* Main subjects */

= Main subjects =

== General ==

* [[Onboarding]]
* [[Biosafety]]
* [[Animals]]
* [[Orders workflow]]

== Experiments ==

* [[Experiments]]