OpenLLM-France/wikimedia huggingface dataset:
# GENtle/Enzyme management

The enzyme editor for enzyme management, both globally and per DNA sequence, is divided into three lists:
* A list of enzyme groups (top right)
* A list of enzymes in that group (bottom right)
* A list of current/temporary enzymes (left)
Enzymes can be copied into/removed from the left list through the <--Add and Remove--> buttons. Enzymes can be deleted from a group (except All) via Delete from group, or added via New enzyme. A double click on an enzyme name in either list shows an enzyme properties dialog.
Enzymes from the left list can be added to a new or existing group via the respective buttons. All enzymes from a group can be added to the left list, and a group can be deleted.
You can share enzyme groups with other GENtle users on your intranet via a commonly shared database. Create an enzyme group as "Database name:Enzyme group name", and it will be available to everyone using that database on the next start of GENtle. Note that when creating the enzyme group, use the name of the database as it appears in your local installation (maybe "Shared", "Shared0", "Shared (2)" etc.).
# GENtle/Graph

The graph module is still in heavy development. It will allow for display of "plotted" data, such as HPLC/FPLC data sets.
# GENtle/Import

The import dialog is a standard "file open" dialog. It can be invoked via Files/Import or Ctrl-I.
Multiple files can be chosen to be imported in a row. GENtle will automatically try to determine the file type, but also a file type can be chosen manually.
Supported formats include:
* GenBank
* GenBank XML
* FASTA
* ABI/AB1 (popular sequencer output format)
* PDB (a 3D format, import as annotated sequence)
* Clone (old DOS program, proprietary format)
* Numerous other sequence formats that will be imported as "sequence only", without annnotations, features etc.
* Comma-separated values (CSV) from various machines (HPLC/FPLC/photometer) for graphs and plots
# GENtle/Options

Global program options can be altered via Tools/Options.

## Global settings

| Option | Description |
| Language | Currently English and German are available |
| Enhanced display | Can be turned off on machines with very show graphics |
| Show sequence title | Displays the sequence title in the DNA map |
| Show sequence length | Displays the sequence length in the DNA map |
| Load last project on startup | Automatically loads the last used project when starting GENtle |
| Use metafile format | Generates a WMF when copying the DNA map instead of a bitmap |
| Show splashscreen | Shows the GENtle splash screen when starting |
| Check for new version on startup | Checks (and downloads) a new GENtle version via internet on startup |
| Use internal help | Help should open in a browser window by default. If that doesn't work, check this option |

## Enzyme settings

Here the gloal enzyme options can be selected. These can be overridden for an individual sequence in the sequence editor, where there is a tab identical to this one.
| Option | Description |
| Use global enzyme settings | Turn most of the other options on this tab on or off globally |
| Join enzymes | In a DNA map, cuts of isoenzymes can be grouped together instead of displayed individually |
| Use color coding | Restriction enzymes can be shown in a color matching their number of cuts in a given sequence. The three buttons to the right of this option each hold a color choice dialog for single, double, and triple cutters. |
| Use min/max cutoff | Shows only enzymes that cut a minimum/maximum times |
| Sequence length | Shows only enzymes with recognition sequences of the selected lengths |
| Use enzyme group | Uses only enzymes from the selected enzyme group |
| Show methylation | Shows DAM and/or DCM methylation in map and sequence, in red |
| Show GC contents | shows the GC contents in the map |
# GENtle/Feature requests

Requested Features:
* Import of Vector NTI Database/Data
* Export of Map as Vector Graphic
* Edit and move around Plasmid Map Layout
* Allow storage in database of complete sequencing files (if space is a concern maybe an upper limit of 2 sequences for each clone would suffice)
* Add sections in the database to allow record of box storage position of clone's DNA, glycerol stock, primers
* Allow closing of files with Ctrl-W
* Clicking a region in the vector map should take the cursor to that region in the sequence viewer.
* Tm and palindromic sequences should show for primers
* The database should be searchable for a protein/nucleotide sequence
* Feature names should be maintained when inverted during ligation
* Selection should be able to be copied as reverse complementary
* "Klenow-filling" should include removal of 3'-overhangs
* Virtual gel for any DNA sequence
# GENtle/Find

The Find dialog in DNA and amino acid sequence can be invoked via Ctrl-F or Edit/Search. It displays can find a string in
* the current sequence
* a feature name
* a feature description
In DNA sequence display, it also look in
* the reverse sequence
* the translated amino acid sequence(s)
* restriction enzyme names
The search is commenced automatically after changing the search string, if it is three or more characters long. For shorter search queries, the Search button has to be clicked.
Single-clicking on a search result will select and display the result in the sequence. A double click will exit the dialog, and open the sequence editor for features, or the enzyme management dialog for restriction enzymes.
# GENtle/Ligation

The ligation dialog is a means for virtually ligating two (or more) DNA fragments. It can be invoked via Tools/Ligation or Ctrl-L.
The left list shows all potential DNA sequences to be ligated. Some of these are automatically selected, but selection can be manually changed. The right list shows the possible products of a ligation of the selected sequences. Some circular products will be shown in two forms (A-B and B-A), which only differ visually.
The selected products will be generated as new sequences on clicking the Ligate button.
# GENtle/FAQ

FAQ - frequently asked questions.
    Q: This manual sucks! And I want one in my language! What can I do?
    A: It's a wiki! You can edit any page and improve the manual yourself. You can even start and maintain a new translation (contact the programmer through this page).
    Q: Why does GENtle try to connect to the internet all the time?
    A: An internet connection is mandatory for BLAST- and ReBase-searches, as well as for the online tools.
    A: At the beginning of each GENtle session, a check for possible updates takes place, which also requires an internet connection. This can be turned off in the Tools/Options menu.
    Q: Why can't I perform a BLAST search for the amino acids coded by the selected DNA sequence?
    Q: Why can't I extract amino acids from the selected DNA sequence?
    A: A reading frame must be selected.
    Q: There's a problem with multiple users using GENtle on my Windows machine.
    A: You might have to allow write access to "local.db" in the GENtle directory for all users involved.
    A: You can turn off the "registry settings bug" via Tools/Options/Register protocols and extensions on startup
    Q: New updates download, but don't install.
    A: You need write access to the GENtle program directory. Alternatively, ask your friendly administrator to download the latest version of GENtle here and install it for you. Remind him that he'll have to do this every few weeks, which might convince him to give you write access...
    Q: I found a bug! And I want new functions as well! Can my favourite protease/marker/restriction enzyme be in the default installation? Where can I donate huge amounts of money for a poor programmer?
    A: Add a bug report or a feature request right here in the wiki, or contact the author of GENtle through the GENtle site.
New proteases to add!
How?
* Open any DNA or amino acid sequence
* Double-click the sequence
* Go to "Proteases"
* Click on "New protease"
* Enter name and sequence (one of the following)

## PreScission

    L,E,V,L,F,Q|G,P
See here for a more detailed description.
# GENtle/Image Viewer

The Image Viewer module can be invoked via Tools/Image viewer. It can display images, such as gel photos, print them, or save them in another image format.
The viewer can read and write common formats, such as JPG, TIF, BMP, GIF, etc. In addition, it can read the IMG format used by the BioRad Molecular Analyst software.
The directory can be selected via the upper left button. The files in that directory are shown below. A single click on a file displays the image.
The context menu of the image contains entries to save or print the image, or copy it to the clipboard. For saving, PNG, TIF, BMP, and JPG are available formats, with PNG being the default, as it has the best lossless compression.
Labels of IMG images are shown on screen, print, and saved images by default. This can be changed through the "Show labels" checkbox beneath the file list.
An image can be inverted (black <=> white) through the "Invert" checkbox.
# ID Board Review/Bacterial Diseases/Mycobacterium
## Medically Significant Mycobacterium Species
### Mycobacterium Tuberculosis Complex

* Mycobacterium tuberculosis
* Mycobacterium bovis
* Mycobacterium leprae

### Non-TB Mycobacterium (NTM)
#### Slow Growers (>7d)
##### Photochromogen

* Mycobacterium kansasii
* Mycobacterium marinum
* Mycobacterium haemophilum

##### Scotochromogen

* Mycobacterium gordonae
* Mycobacterium scrofulaceum
* Mycobacterium szulgai

##### Nonchromogen

* Mycobacterium avium complex (MAC)
* Mycobacterium ulcerans

#### Rapid Growers (<7d)

* Mycobacterium fortuitum
* Mycobacterium abscessus
* Mycobacterium chelonae
# ID Board Review/Bacterial Diseases/Musculoskeletal Infections

The ABIM ID blueprint does not elaborate on which specific Bacterial Musculoskeletal Infections will be tested. As such, please understand that this page is filled with topics that the Wikibook author(s) believe are likely to be high-yield based on their knowledge, and not strictly based on the ABIM blueprint.

## Musculoskeletal Infections

* Myositis
* Necrotizing Fasciitis
* Septic Arthritis
** Prosthetic Joint Infection
# ID Board Review/Bacterial Diseases/Musculoskeletal Infections/Septic Arthritis

This page is for native joint infections. See Prosthetic Joint Infection for artificial joint infections.

## Etiologies

* S. aureus
# ID Board Review/Bacterial Diseases/HACEK Organisms

This is a group of fastidious, Gram-negative bacilli that can cause Infective Endocarditis. Because of their fastidious nature, they often require a longer period of time to grow on culture media and are held for 10 days (instead of the usual 5 days).
* Haemophilus spp
* Aggregatibacter actinomycetemcomitans
* Cardiobacterium hominis
* Eikenella corrodens
* Kingella kingae
# ID Board Review/Bacterial Diseases/Head and Neck Infections

The ABIM ID blueprint does not elaborate on which specific Bacterial Head and Neck Infections will be tested. As such, please understand that this page is filled with topics that the Wikibook author(s) believe are likely to be high-yield based on their knowledge, and not strictly based on the ABIM blueprint.
* For Eye Infections, please see Ophthalmologic Infections
* For Oral Infections, please see Gastrointestinal Infections

## Facial Infections

* Periorbital Cellulitis

## Ear Infections

* Otitis Externa
* Otitis Media

## Nasal and Sinus Infections

* Sinusitis
# ID Board Review/Bacterial Diseases/Musculoskeletal Infections/Septic Arthritis/Prosthetic Joint Infection
## Etiologies

* S. aureus
# Inclusive Data Research Skills for Arts and Humanities/How to add a chapter

Each page linked to this Wikibook is called a chapter. Here you will learn how to add a new chapter to the book, starting with adding it to the list of content and then adding text. If you title you want to write is already present, you can skip step.
The information is also available as a video.
* On the title page of the Wikibook, scroll down to the 'Contents' section.
* Click 'edit source' next to the section you want to add your chapter to.
* Copy this text complete with the asterisk: *[[/Your title here/]]
* Paste the text into the section, scroll down and click the blue 'Publish changes' button
* The title of your chapter will appear in the table of contents. Click on it to go to the new page.
* You will be taken to a new page; to enter the visual editing mode you can either click 'Create' at the top of the page or look for the pencil icon on the right and select the 'Visual editor' option.
* This will take you to the visual editor, which is a 'what you see is what you get' interface like writing an email or a word document.
* You can start writing straightaway. Save your changes by clicking the blue 'Publish page' or 'Publish changes' button in the top right.
    Top tip: Use the 'Publish changes' button often! It is the equivalent of your save button, and you don't want to risk losing what you are writing if your computer crashes, you accidentally close the window, or a cat helpfully turns off the wifi.
https://www.youtube.com/watch?v=YOmBhiMn6g0
# Inclusive Data Research Skills for Arts and Humanities/How to create an account

To fully take part in this collaborative book, we recommend creating an account. This will help with attribution and make the writing process easier as you gain extra permissions over time.
If you already have a Wikipedia account, the log in details will also work on Wikibooks
At the bottom of this page is a video demonstrating how to create an account. You can also follow the step-by-step process written below:
* Go to the Outreach Dashboard for this Wikibook: https://outreachdashboard.wmflabs.org/courses/Introduction_to_WikiBooks/Inclusive_Data_Research_Skills_Hackathon_for_Arts_and_Humanities?enroll=rcaukxzp
    The Dashboard gives an overview of what edits are made, and acts as a feed showing what edits have been made.
* Click on the button labelled 'Sign up with Wikipedia'. This will take you to a signup form on Wikipedia.
* Start by picking a username. Please use something anonymous; all edits are public, so it is easier to start anonymous and link to your real identity than the other way round.
    Note: Don't pick something which could imply the account is shared. For example, 'User:Social media manager' could indicate that several people have access to the account, which makes attribution harder.
* Pick a unique password.
* Though it is optional, we recommend providing an email address in case you forget your password.
* Click 'create your account'.
* Return to Wikibooks and refresh the page to check you are logged in. If you are not logged in yet, click log in in the top right and use the details of the account you just created.
* And finally: welcome to Wikibooks!
https://www.youtube.com/watch?v=-zk-p6940i0
# Inclusive Data Research Skills for Arts and Humanities/How do you get funding?

There are various ways to get research funding for arts and humanities researchers. One of the main funding bodies for this field is the Arts and Humanities Research Council (AHRC), who have various funding rounds for different purposes

## Where can I find previously funded projects?

Exploring previously funded projects is a great way to discover the types of projects that have been funded. The UKRI gateway (2024) to publicly funded research and innovation is an interactive tool with a search function. Users are able to search for projects by key words, subject, project team members and the project reference. Each project then includes:
* Project title
* Lead research organisation
* Department name
* Abstract
* Organisations linked to the funding
* People on the funding
* Funded value
* Funded period
* Funder
* Project status
* Project category
* Project reference
* Principle investigator
* Research subject
* Research topic
UKRI has a ‘funding finder’ for searching current opportunities; this is a great place to start looking for funding. Some of these opportunities are very specific, others more general. You can also contact UKRI if you aren’t sure if your project is right for a specific research call.
As UKRI is a publicly funded body, all the projects that successfully received its funds can be searched; on this page, you can see who was involved in this project and what institution they were part of when the project was initially funded.
https://gtr.ukri.org/

## Finding UKRI Funding

UKRI has a ‘funding finder’ for searching current opportunities; this is a great place to start looking for funding. Some of these opportunities are very specific, others more general. You can also contact UKRI if you aren’t sure if your project is right for a specific research call.
https://www.ukri.org/opportunity/

## Overview of AHRC open grants

As part of the DAReS project, our post-doc researcher prepared this presentation about AHRC ‘open grants’; this can be a good place to start looking for applying for funding and thinking about what stage of research you are at.
research funding presentation

## References

UKRI gateway (2024). UK gateway search page
# Inclusive Data Research Skills for Arts and Humanities/Guidance on accessibility and good practice

Access is complex and there are multiple approaches to understanding it. Ellcessor (2016) writes:
   First, access must be understood not in terms of availability, affordability, or choice but in terms of an individual’s ability to engage meaningfully with a medium/technology and its content; second, a hegemonic user position is created by digital media technologies and their usages, and this user position is not neutral but perpetuates an able-bodied norm and contributes to inequalities of access.
By this Ellcessor places emphasis on meaningful engagement. Metaphorically, people cannot just be allowed in, they must be able to participate. Second, Ellcessor (2016) draws attention to the fact that digital technologies assume a particular user - usually a white, non-disabled, man. Good inclusive practice means not making this assumption.
In addition to accounting for a wide range of users and experiences of the world, good access practice understands accessibility, as practiced within disability communities, as a world-making practice that reshapes the material, digital and social world. Access is not a friction-less, self-evident good, that integrate disabled people into the non-disabled world without questioning the utility and ultimate good of that world.
More practically, the first and often most effective tool of access is always communication. Providing whoever you engage with, whether students, other researchers, the public or partners with clear information about where you'll be, what you'll be doing and what will be expected of them is a great starting point. This requires you to think carefully about the assumptions that you make what is involved in an activity. Those assumptions are likely embedded in your culture and quite possibly your assumptions about how bodyminds work.
Make sure you've given yourself a lot of time before the thing you are doing. There has to be time for conversation. Then, ask people what they need. Access can be expansive. This can go beyond how people's bodyminds do and don't conform to societal functions. Asking what people's access needs are can be as simple as asking, 'what do you need to do your best work'? Then respond, as best you can, with grace and curiousity. Access often challenges our deeply held and felt understandings of what 'good work' and 'politeness' is. This is challenging, but also part of the joy of access world-making.
In digital spaces, Wikimedia is pretty accessible. But all that work to build an accessible website doesn't count for anything if you don't write the alt text. Write the alt text.
* ↑ "Restricted Access". NYU Press. Retrieved 2024-01-26.
* ↑ "Building Access". University of Minnesota Press. Retrieved 2024-01-26.
* ↑ "Accessibility in the Arts: A Promise and a Practice". promiseandpractice.art. Retrieved 2024-01-26.
# Inclusive Data Research Skills for Arts and Humanities/DAReS Codesigners
## Co-Designers

The DAReS co-designers are at the heart of this project and their thoughtful, engaged contributions have pushed the boundaries of how inclusion and arts and humanities focused data and digital research skills can be understood. This project would not exist without them and with thanks to each of them, they are:
| Yutong Wu | Maribel Hidalgo Urbaneja | Hossein Mousavi |
| Syeda Sana Batool | Maria Golovteeva | Hannah Gardner Seavey |
| Scarlet Clark | Leah Junck | Grace Cappy |
| Sarah Qian Gong | Laura Wain | Christine Gibson |
| Sandip Kana | Kelsie Acton | Cai Tuomivaara |
| Pushpi Bagchi | Karen Hanrahan | Beth Bramich |
| Panrawee Paisarnnan | Joseph Young | Annie Mackinnon |
| Olawale Oni | Jaime Prada | Ana Teles |
| Nina O'Reilly | Ishan Jha | Adebukola Olatunji |
| Marika Grasso | Hoyee Tse | |
# Inclusive Data Research Skills for Arts and Humanities/Data practices

Object of study > Data Problem(s)
Research Methods :
| Gather | Access | Analyse |
| Example | Example | Example |
| Example | Example | Example |
| Example | Example | Example |
Data/Digital tools & methods :
| Gather | Access | Analyse |
| Example | Example | Example |
| Example | Example | Example |
| Example | Example | Example |
# General Mechanics/Force and Motion

Year 10 Force and Work 7 periods
* Possible Approach:
* Lesson Suggested Learning Outcomes Course Outline Resources
* 1 – 3  Recognise that unbalanced forces cause acceleration.
*  Investigate the relationship between the unbalanced force acting on an object, is mass *and acceleration: Newton’s Second Law. (Use Fnet = ma giving correct units for all quantities)
•**Reinforce ideas about force causing acceleration (= the rate at which speed changes)
* Experiment 1: Finding the force required to move an object (static friction)
* Discuss the factors that may affect the frictional forces acting on the block (e.g. load on *the block, surface area in contact with the bench, type of the surfaces in contact …)
* Attach a force meter to a block at rest on the bench. Pull the force meter and slowly increase *the force until the block just begins to move – record the force meter reading, tabulate data, *repeat, calculate average.
* [Or, use a bag to which washers may be added, attached to a cord and hanging over the end of *the bench to pull the block.]
* quantities and the third unknown) – a three symbol triangle may simplify the maths.
****** Homework: Coursebook – Newton’s second Law
****** force (e.g. when a force acts on a body, it moves faster and kinetic energy increases)
****** • Introduce the relationship between energy transferred and work done.
****** • Define work done in terms of the applied force and the distance through which this ********force acts (Work done = force x distance)
* Explore the relationships between science and technology by investigating the application of *science to technology and the impact of technology on science, e.g. Archimedes’ screw to *illustrate the principle of oits use in water irrigation or the use of springs and similar *propulsion devices in toys
* Experiment 4: Stretching Springs
* Hang a spring vertically using a clamp and stand. Add weights to the end of the spring, *measure the length of the spring after each additional weight is added. Calculate the *extension (Note: some initial weight will probably need to be added before the spring *stretches at all) Graph extension vs applied force. Interpret the graph, e.g. find the *extension for unit applied force or applied force per unit extension.
* Discuss and brainstorm ideas about what causes things to turn about a pivot (fulcrum).
****** • Introduce the concept of the turning effect of a force (torque).
****** • Discuss the concept levers – to increase the turning effect, use a greater distance *******(e.g. a long crowbar) and/or a greater force (e.g. a heavier weight)
****** • Use the lever rule to calculate forces and distances at right angles to the applied ********force (given three quantities and the fourth unknown).
* Experiment 5: The turning effect of a force
* Kit available from the science Office
****** • Homework: Coursebook – The Turning Effect of a Force
* Extension