OpenLLM-France/wikimedia huggingface dataset:
# GENtle/Bug reports

    Note: You can also write email to report a bug. Please see this page.
Linux (Ubuntu 8.10 with MySQL 4.1 installed extra), GENtle v. 1.9.3
* please update the software so that it can cope with MySQL 5, MySQL is already outdated and difficult to install on current Linux systems
* When using the PCR tool, adding primers (that have been loaded from the database first) causes a program crash, so the PCR-tool option is unfortunately not usable...
This is the output on the console:
Bernd (talk) 12:51, 20 January 2009 (UTC)
Using GENtle on WinXP Pro. Attempting to BLAST anything results in immediate shutdown of the software. No prompting for save or anything... Any suggestions? Patches?
    Fixed in CVS, will go live with the next version. --Magnus Manske 14:33, 30 January 2007 (UTC)
Under Mac OSx 10.4.8 (PPC platform), when starting GENtle the program hangs while displaying the introductory splash screen.
    I can not reproduce this bug on my G4 PowerBook (PPC, 10.4.8). It also runs well on PPC iMac 10.3.9. Was GENtle installed under the same user name you're using? It could potentially be a write access conflict. --Magnus Manske 14:33, 30 January 2007 (UTC)
Under OpenSuSE 10.2 x86 the CVS version GENtle builds and works fine. One problem: when blasting a sequence GENtle hangs. Probably a threading issue? This is also the case on OpenSuSE 10.2 x86_64. Follow-up: I tested the latest CVS version (17 Feb 2009) on openSUSE 11.0 and openSUSE 11.1, both x86 and x86_64. Still, when BLASTing anything, GENtle hangs. I used wxWidgets-2.8.9.1 to build. I can send you additional data if you like.
# GENtle/Calculators

The calculator module can be invoked via Tools/Calculator. It contains several specialized spreadsheet-based calculators for typical tasks in molecular miology. The editable fields are shown in blue, the (major) results of the calculation are shown in red.

## Ligation calculator

This calculator gives the amount (in µl) of vector and insert for a ligation, based on the length and concentration of each respectively, their desired ratio and total mass of DNA. A typical ratio of insert:vector is 3:1

## DNA concentration calculator

This calculator gives the amount and purity of DNA based on photometric absorption at 260 and 280 nm, respectively, as well as the dilution (in case one measures a 1:100 dilution of the original DNA sample) and a correction factor for different types of nucleic acids.

## Protein calculator

This calculator gives the amount and purity of peptides/proteins based on photometric absorption at 250 and 280 nm, respectively, as well as the molecular weight of the peptide, the layer thickness of the cuvette used, and the number of tryptophanes, tyrosines and cysteines in the peptide.

## Data

This shows a codon table and a reverse codon table, both for standard code. This page can not be edited.
# GENtle/DNA

Within the DNA module, DNA sequences can be viewed, edited and annotated. It is the central module of GENtle. Two major components of the DNA module are the DNA map and the Sequence map; see there for details.

## Open and display DNA

A DNA sequence can be opened in one of the following ways:
* Open from a database (see Databases)
* Import from file (see Import)
* Manual input (see Enter sequence)
* Create from another DNA module

## Toolbar

Several functions and display options can be invoked in the tool bar:
* Enter sequence
* Open sequence
* Save sequence
* Undo
* Cut
* Copy
* Paste
* Toggle linear/circular
* Show/hide open reading frames
* Show/hide features
* Show/hide restriction sites
* Expand (=show only) map
* Toggle edit mode
* Zoom

## Detail tree

The detail tree, left of the DNA map, shows all parts of the current sequence, including features and restriction enzymes, in a structured fashion. Features and restriction enzymes can be toggled in visibility by a double click, or further manipulated through the context menu.

## Special menus

| View/Show 3'->5' | Show the complementary DNA strand in the sequence map |
| Edit/Edit ORFs | Change the settings for open reading frame display |
| Edit/Show possible sequencing primers | Opens the Sequencing Primers dialog, which can add possible sequencing primers as features |
| Edit/Remove sequencing primers | Removes all sequencing primers generated by the above function from the sequence |
| Edit/Auto-annotate sequence | Finds features from common vectors and other databases in the current sequence |
| File/Print map | Prints the DNA map |
| File/Print sequence | Prints the Sequence map |
| File/Print report | Prints a brief overview. See Printing |
# GENtle/Dot plot

Dot plots can be generated in GENtle between two DNA sequences, which can be selected from drop-down lists in the toolbar. The calculation of the dot plot will start immediately and take a few seconds, depending on the length of the sequences.
A window size and a mismatch limit can be chosen as pararmeters for the dot plot. A click into the plot will take you to the respective position in sequence 1 (the first dropdown box), unless "Open sequence 2" is selected.
Either sequence can be opened via the context menu at the respective position. Also, the plot image can be copied or saved via the context menu.
# GENtle/Automatic annotation

The automatic annotation feature can search a database of standard vectors (included with the GENtle package), and (optionally) a user-generated database, for feature sequences that are found in the currently opened DNA sequence. Recognized features are then annotated in the current sequence.
Invoked through Edit/Auto-annotate sequence or F9, a dialog opens, offering various settings:
* Whether or not to search the common vectors database
* Whether or not to use a user-generated database (and, if so, which one)
* Whether or not to reduce the number of generated features (recommended; otherwise, a lot of features are annotated)
* Whether or not to add unrecognized open reading frames as features
# GENtle/DNA markers

This file contains DNA markers for virtual gels. You can add your own in the following form:
    Name:amount,bp:amount,bp:amount,bp:amount,bp: ...
    *Name is the name of the marker.
    *bp is the number of base pairs in that band.
    *amount is the amount of DNA in that band if 500 ng of the marker is loaded per lane (ng).
    ":amount" can be omitted. The default amount (20) is then used.
Markers you enter will be used in the next GENtle release!
# GENtle/Edit primer dialog

This dialog assists in optimizing a primer. For that reason, many variants of the primer are generated and can be examined.
The center line of the dialog shows the current variant of the primer; details of that variant are shown in the upper right box. OK will end the dialog, committing that variant to the PCR module. Cancel will end the dialog and not change the PCR module. Reset will return the primer in the dialog to the variant the dialog was originally started with.
The list in the lower half of the dialog contains an automatically generated list of variants of the current primer, sorted by an arbitrary score. The "region" of variants can be influenced by multiple settings in the upper left quarter of the dialog. Available settings include:
* The variation of the 5'-end of the primer to the right and to the left.
* The variation of the 3'-end of the primer to the right and to the left.
* The minimum and maximum length of the primer.
* The minimum and maximum melting temperature of the primer.
Any change of these settings will trigger a recalculation of possible variations. These variations are then evaluated and shown in the list in the lower half of the dialog. Double-clicking one of the variations will change the current variation in the center line, and the properties display in the upper right quarter of the dialog.

## Properties display

This will display:
* The primer sequence in 5'→3' orientation
* The ΔH and ΔS values
* The length and GC contents of the primer
* The melting temperature, calculated according to the Nearest Neighbour method (usually best results, but only for longer primers)
* The melting temperature, calculated according to the salt-adjusted method (medicore results)
* The melting temperature, calculated according to the GC method (simplicistic)
* The highest self-annealing score (arbitrary) and the display of that annealing
    Caveat : Calculating primer melting temperatures is tricky. If one of the three methods gives a totally different result than the other two, ignore it. Also, the melting temperature is only calculated for the 3'-end of the primer that anneals with the sequence!
# GENtle/Command line options

GENtle can be called from the command line/shell/DOS box. You can automatically import and open files by adding them to the command line:
New parameters as of version 1.8.6:

## --view-sequencing-start=X

    When auto-opening an alignment, show only the sequence from position X on (first position=1)

## --view-sequencing-end=X

    When auto-opening an alignment, show only the sequence up to position X on (first position=1)

## --view-sequencing-reverse-complement

    When auto-opening an alignment, show the reverse complement sequence

## --no-splash-screen

    Do not show splash screen

## --no-tips

    Do not show tips
# Emulation/Mega Drive
## About Mega Drive

The Sega Mega Drive was a popular console in the 1990's, and continued to be a popular console in some geographic regions well into the 2010's.

## Sega Mega Drive and Genesis Emulators
### SEGA Mega Drive and Genesis Classics

An official emulator and ROM pack developed by SEGA. Includes over 50 officially licensed games as well as an easy to use launcher. ROMS included are compatible with other emulators.
Steam Page

### Gens

Gens is an open source Genesis emulator.

### DGen

DGen is an open source Genesis emulator.

### GPGX

An open source Mega Drive emulator focused on accuracy.

### PicoDrive

A source available Mega Drive emulator.

## Refrences

* ↑ "You Can Buy Sega Genesis Roms! Mega Drive And Sega CD". Retrieved 29 July 2021.
* ↑ "GitHub - notaz/picodrive: Fast MegaDrive/MegaCD/32X emulator". GitHub. Retrieved 29 July 2021.
# Emulation/N64
## About the Nintendo 64

As one of the first widespread 3D focused game consoles, the Nintendo 64 was host to a number of groundbreaking software titles which were historically and culturally important.

## Nintendo 64 emulators
### Project64

Project64 - Widely used open source Nintendo 64 emulator.

### Mupen64Plus

Mupen64Plus - Open source emulator.

### Other Emulators

* 1964 - Open source emulator for Windows. More modern then other historic emulators, it was once quite popular.
* ParaLLEl RDP - Retroarch core for fast RDP emulation.

### Historic Emulators

* Nemu64 - Historic emulator.
* Project Unreality - Historic emulator, and perhaps the first legitimate working Nintendo 64 emulator. Now only used out of historic interest.
* UltraHLE - A pioneering historic emulator. Now only used out of historic interest.
# Emulation/Nintendo 3DS
## About Nintendo 3DS

The Nintendo 3DS is a handheld game console that was popular throughout most of the 2010's. Fitted with an autostereoscopic display, the 3DS developed an impressive library of culturally relevant games and software.

## Citra

Citra is an open source emulator for Nintendo 3DS software that can run under a number of operating systems. It has decent compatibility with commercial titles.

## Hardware

It may be desirable to use a stereoscopic display when emulating a 3DS to take advantage of the 3D effect.
# Emulation/On Dreamcast/Burning MAMED on a Mac

Back to Emulation
* Start with a big stack of blank disks (you may need them)
* Get Toast (cd burning application)
* Download DC Mac Pac
# Emulation/Nintendo DS
## About the Nintendo DS

There are significant software and hardware differences between the original DS / DS lite and the DSi. The DSi features a processor twice as fast as the prior models, and also sports four times as much RAM.

## Nintendo DS Emulators
### melonDS

melonDS is an open source and performant Nintendo DS emulator. Supports DSi games, microphone input, and local Wi-Fi emulation.

### DeSmuME

DeSmuME is a popular Nintendo DS emulator. It is open source and runs under many operating systems.

### DraStic

DraStic is a proprietary (closed source) Nintendo DS emulator. Available on Android, it costs money to buy.

### No$GBA

No$GBA is a freeware (Gratis) Game Boy Advance and Nintendo DS emulator. Supports DSi emulation.

## Hardware Considerations

It may be best to use a device with a touch input for Nintendo DS emulation.
# Emulation/Nintendo Switch
## About the Nintendo Switch

While the Switch uses a great deal of custom hardware, its computer is very well understood. This is because it is based on a SOC which was also used in other products, making its technical details much better known and accessible than the computer hardware of most consoles.

## Nintendo Switch Emulators
### Yuzu

Yuzu is an open source emulator for Nintendo Switch software that can run under Windows and Linux. It has some compatibility with homebrew and commercial titles.

### Ryujinx

Ryujinx is an open source Nintendo Switch emulator.

### Skyline

Mobile specific emulator for Android with limited compatibility. HLE open source emulator.

### Strato Emulator

Strato Emulator is an open-source compatibility layer for the Nintendo Switch that runs on Android. It is a fork of Skyline Emulator that focuses on the continuation of the original project as Skyline Emulator's development has been put on halt due to copyright reasons.

## Hardware considerations

Many major Nintendo Switch games used the touchscreen sparingly, if at all. Thus touch input hardware on the host system is somewhat less important than for other handhelds.
JoyCons, and other switch controllers typically connect over Bluetooth, with some controllers supporting wired USB communication. Both are common standards.

## Software considerations

As with any emulator, the primary use of a Switch emulator is to maintain backups of games you own. They can also be used to run and develop homebrew.
The open source Mesosphere firmware is capable of booting some commercial games.

## References

* ↑ "GitHub - Ryujinx/Ryujinx: Experimental Nintendo Switch Emulator written in C#". GitHub. Retrieved 29 July 2021.
* ↑ "Skyline is an in-development Nintendo Switch emulator that actually works". XDA. 1 May 2022. https://www.xda-developers.com/skyline-is-an-in-development-nintendo-switch-emulator-that-actually-works/.
* ↑ "skyline-emu/skyline". Skyline. 7 May 2022. Retrieved 7 May 2022.
* ↑ "Strato Emulator - Best Nintendo Switch emulator for Android". 2023-06-30. Retrieved 2023-07-28.
# Emulation/On Dreamcast

* Burning MAMED on a Mac
* Burning discs on a Mac

## External links

* DCNews– Dreamcast Emulation and Gaming news
* Dreamcast Emulation – A repository of Dreamcast emulation, tools, and software
* Dreamcast-Scene – A website dedicated to independent Dreamcast software
# Emulation/NES
## About the Nintendo Entertainment System

The Nintendo Entertainment System and Famicom are historically and culturally important home video game consoles of the 1980's. A number of important series either saw their start on the Famicom or NES.

## NES emulators
### FCEUX

FCEUX is an open source NES emulator.

### PuNES

PuNES is an open source and highly accurate emulator.

### Mesen

Though the open source Mesen was discontinued in 2020, it is commonly considered among the best NES emulators. It is noted for its ability to apply 3rd party texture packs to games, greatly enhancing graphical fidelity and creating a remix culture of sorts among its users.

### Nestopia

Nestopia is an open source NES emulator focused on accuracy.
As of 2021 the original project is abandoned, but it's successor fork Nestopia UE (Undead Edition) remains relevant.

### Others

* NESticle - An early freeware emulator for DOS and Windows 95 based PCs. Now only used out of historic interest or on low spec PCs from the early 1990s.
# Emulation/Mac
## About the Mac

Classic Mac systems can run a number of historically important software.
# Grand Theft Auto: Liberty City Stories/Grease Sucho
## Prerequisites

* Missions: Big Rumble in Little China
* Location: Cipriani Restaurant, St.Marks District, Portland

## Walkthrough

This mission requires you to win in a streetrace against a streetracer named Sucho who Ma describes as "good to his mother". You will need a fast car for this mission. The Hellenbach GT from Snuff is preferable, but the Leone Sentinel or a Police Car can both be used.
Once the race has been completed, you are required to kill the racer. Once that is done, the mission is completed.

## Tips

* You can also get the Hellenbach GT from the showroom if you've done level 4
* You should keep Sucho's car if you can. You will need it later if you are doing Love Media Garage.

## Reward

* $1000
# Grand Theft Auto: Liberty City Stories/Blow up 'Dolls'
## Prerequisites

* Missions: A Volatile Situation
* Location: JD's strip club, Red Light District, Portland

## Walkthrough

Rig a Sindacco car with explosives and blow up an enemy casino. This is a nice easy mission compared to the last one. After the cutscene go out front and there should be a Sindacco car waiting out there. Take the car to 8-ball's bomb shop(behind the car dealership). Then carefully drive it to the casino. If you have the right car then the Sindaccos will let you in. Park the car in the garage and run out of the casino area. Once it tells you to blow the bomb, do it. Now sit back and watch a nice cutscene of a guy running aroung while on fire.

## Tips

* If you don't have the right kind of car then the Sindaccos will start to shoot you.
* If you do too much damage to the car then you will blow up the car with the bomb in it.

## Reward

* $5000 (nice!)
* You're done with JD for a while
# Grand Theft Auto: Liberty City Stories/Dead Meat
## Prerequisites

* Missions: Grease Sucho
* Location: Cipriani Restaurant, St.Marks District, Portland

## Walkthrough

A disappointed Ma informs Toni that she's put a hit on Toni, with some hit men on the way to kill him.

## Reward

* $0
# Grand Theft Auto: Liberty City Stories/Don in 60 Seconds
## Prerequisites

* Missions: Bone Voyeur
* Location: JD's strip club, Red Light District, Portland

## Walkthrough

You have to drive Salvatore Leone back to his mansion without the cops getting him. Get in his car and immediately turn around and go to the Pay-N-Spray. You will have a wanted level by now. After that just drive to his mansion without getting another wanted level and you beat the mission.

## Tips

* You don't have to go to the Pay-N-Spray in this mission but it is a good idea
* You have to use Mr.Leone's car. If you break it then you fail

## Rewards

* $0?
* Mr Leone can now give you missions
# Grand Theft Auto: Liberty City Stories/Controls
## On Foot

| PlayStation 2 | PlayStation Portable | Action |
| Left Control Stick | Left Control Stick | Move Character |
| Right Control Stick | L1 + Left Control Stick | Move Camera |
| X | X | Sprint |
| Square | Square | Jump |
| Circle | Circle | Fire Weapon |
| Triangle | Triangle | Enter Vehicle |
| L1 | L1 | Look Forward |
| R1 | R1 | Aim Weapon |
| R1 + L3 | R1 + D-Pad (Down) | Free Aim |
| L2 | D-Pad (left) | Cycle Weapons/Targets Left |
| R2 | D-Pad (right) | Cycle Weapons/Targets Right |
| R3 | L1 + R1 | Look Behind |

## In Vehicle

| PlayStation 2 | PlayStation Portable | Action |
| Left Control Stick (left and right) | Left Control Stick (left and right) | Steer Vehicle |
| Left Control Stick (up and down) | Left Control Stick (up and down) | Lean Forward/Backward |
| Right Control Stick | D-Pad (left and right) | Turret Control |
| X | X | Accelerate |
| Square | Square | Brake/Reverse |
| Circle | Circle | Fire Weapon |
| Triangle | Triangle | Exit Vehicle |
| L1 | D-Pad (left and right) | Change Radio Station |
| R1 | R1 | Handbrake |
| L2 | L1 + Left Control Stick (left) | Look Left |
| R2 | L1 + Right Control Stick (left) | Look Right |
| L2 + R2 | L1 + Left Control Stick (down) | Look Behind |
| L3 | D-Pad (down) | Horn |
| R3 | D-Pad (up) | Sub-Mission |
# Grand Theft Auto: Liberty City Stories/Big Rumble in Little China
## Prerequisites

* Missions: Snappy Dresser
* Location: Cipriani Restaurant, St.Marks District, Portland

## Walkthrough

You get to kill some Triads because your Ma thinks your scared. Get in a car and drive over to Chinatown. Ram the Triad's van and they will come out. Run over all of them. Go to Punk Noodles and keep on going. In a blocked alley there will be some Triads. Kill them with a micro-SMG and you beat the mission.

## Reward

* $0 (You get to hear the theme song)
# Grand Theft Auto: Liberty City Stories/Home Sweet Home
## Prerequisites

None

## Walkthrough

Drive Vincenzo to your safehouse. Then get out and go into your house. Walk into the clothes icon to change into Leone's Suit. Go back outside and if you need to get a feel for the city then you should do that now. Drive Vincenzo to his place in Atlantic Quays.

## Rewards

* $100
* Your safehouse becomes available
# Grand Theft Auto: Liberty City Stories/Bone Voyeur
## Prerequisites

* Missions: Hot Wheels
* Location: JD's strip club, Red Light District, Portland

## Walkthrough

You have to collect money from JD's girls so he can pay you the money he owes you. Get in the van with JD. You have to get $750 from his girls in a certain time limit. This will take about 6 or 7 girls. Some will just be standing on the street so pull up to these and they will dish out the money. A few are with their "customers". Ram the car and she will come out. One is with a pimp, so kill him and then collect her money.

## Tips

* You cannot wear Leone's Suit to do any of JD's missions or the Sindaccos will suspect something
* All of the girls are in the Red Light District
* Don't run over any girls or you don't get their money

## Reward

* 500
# Grand Theft Auto: Liberty City Stories/Dealing Revenge
## Prerequisites

* Missions: Slacker
* Location: Vincenzo's Place, Atlantic Quays, Portland

## Walkthrough

The dealer from Slacker was killed! You have to get revenge. Drive to Chinatown and park in the yellow marker. After you talk to the Sindacco gang member, kill him. Then kill the other two Sindacco members and you have beaten the mission.

## Tips

* If you get the bat outside your hideout then it will be much easier to kill the first Sindacco
* If you get back in your car after you kill the first one then you can just run over the other two but watch out for getting busted by the cops

## Reward

* $500
# Grand Theft Auto: Liberty City Stories/Hidden Packages

File:GTA LCS Hidden Package.jpg

## Portland

* back alley opposite Paulie's Revue Bar.
* Opposite the hospital behind a car, Portland
* behind Ammunation, St. Mark's
* Behind the house on the docks in the first mission's area
* in the rusted car behind 8-Ball's garage
* In the bushes outside the school hall, Callahan Bridge
* Bus depot behind one of the buildings, Portland harbor
* Hanging above a cliff, Portland beach
* in between two Packers, Portland harbor
* on the upper balcony of Marco's Bistro
* on top of a storage container, Portland docks
* on the pier behind Vincenzo's place