# Pathology 2

> [TOC]
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## Abstract
A Pathology revive fixing some of its issues. Unifies the systems that are currently in the code (legacy pathology, diseaschems/viruses) and make disease code a little better^TM^. Creates a new job that revolves around short but lots of interactions with the crew and station. Introduces new mechanics borrowing real life genetic engineering approaches.
:::warning
I am by no means an expert just like genetic engineering/synthetic biology. And while we are at it let people learn something while they create a cure for whatever space has to offer.
:::
## Goals
* Make Pathology a system that is useable for nonantags and actually supports the crew
* Balance focus between analysis/cure and creation of pathogens more towards the analysis
* Reduce the RNG based nature
* Make Pathology more player accessible
* Reduce the dependance on Pathology/Pathologist in case of an outbreak

## Non Goals
* Allow for easy server wipes with no build up.
* Add a job/mechanic that incentivises ~~a genetics/toxins playstyle~~ staying locked up in one room conjuring weapons of mass destruction.
* Incentivise excessive isolation from other players for quarantine purposes

## What needs to be done?
This would be a large project so basically everything needs to be done :sweat_smile:
### Code overhauls and new feature
### Mapping
- [ ] Prefabs
- [ ] overhaul existing pathology prefab
* plans for pathology equipment
* randomly colored hazmat suits
*
- [ ] new dedicated trader with thematic station
*
- [ ] Adventure Zone/s (LRT)
- [ ] Recently abandoned CDC facility
* Facility
* R&D for emergencies
* Shipments prepared for \<previous station name\>
* Old pathology machines \(fake objects\)
* Spanws NPCs and infects them with a high tier pathogen \(set list for visual effects\). The NPCs wont be accessible but someone rushing there should be able to see the event unfold.
* Note to CDC Command: Dont accept improperly secured crates. We suffered an unacceptable outbreak within our lab. We got it contained for now but have to quarantine the infected department. We will evacuate the area for now and send in a cleaning squad. They should arrive in about 20 minutes
- [ ] Adventure Zone/s (Telesci)
- [ ] Syndicate bioweapon test
### Spriting

#### Lab equipment
- [ ] Hazmat Suits
- [ ] Orange \(Bio/chem\)
- [ ] White \(Cleanroom\)
- [ ] Blue \(Bio\)

#### HUD Elements
- [ ] Immune response status effect icon
- [ ] ProDoc UI Icon

### Balancing
---
## Pathogens

### TL;DR
* Main focus is to analyze and categorize pathogens for a profit and to collect characteristics useful in a custom pathogen
* Gives a variety of effects with ways to deal with them according to the pathogen type.

### Pathogen types overwiew (Balancing changes are to be expected)

| | Virus | Bacteria | Parasite* |
|:------------------------------:|:-----:|:--------:|:---------:|
| Duration (max) | 5min | ∞ | ∞ |
| Self immunization possible | Yes | No | No |
| Can be supressed | Yes | Yes | No |
| Vaccinable | Yes | Yes | No |
| Affects multiple areas of body | Yes | No | Yes |
| Stages per infection (max) | 3 | 5 | 2 |
| Characteristics per stage | 2 | 3 | 1 |
| Can be added to food | No | Yes | Yes |

\* Technically referes to something that harms the host but symbiotic relationships should also be possible.
TODO find better name for parasites

### Virus
Small piece of genetic information made to temporarily hijack a hosts cellular machinery to produce a protein complex capable of affecting the host.
#### Effect on player
Short duration with focus on possibly being highly transmissable instead of having a strong effect.

#### Possible methods of delivery
* Injecting into the bloodstream (smoke powder also counts).
* Being in range while transmitting characteristics are active in range of another player (max range is an adjacent tile and viruses dont linger in the air).
* Being hit by a contaminated weapon dealing cut damage.
* Touch reaction of contaminated blood/touching bloody objects.
#### Protection
* Can be vaccinated against and surpressed from progressing but not actually be cured. Though supressed its time is still ticking making it possible to not suffer any actualy symptoms.
* Biosuits prevent touch reaction.
* Gloves prevent touching bloody items.
* Masks prevent inhalation.
### Bacterium
Once infected theyll start to multiply inside the affected persons body until they reach a certain size. Their more complex design allows for showing multiple symptoms.
#### Effect on player
Long effect duration with high amounts of customizability in both spread and symptoms. Can be used to give an ability to the user triggering the symptom in the current stage. Needs to be treated with chems to be permanently removed from the infected person.
#### Possible methods of delivery
* Injecting into the bloodstream
* Same as virus: Being in range while transmitting characteristics are active in range of another player (max range is an adjacent tile and viruses dont linger in the air).
:::info
Unlike with viruses, a bacterium is only transmitted by an emote if the "cause" of the emote is infected (lungs -> cough, sneeze ... | skin -> hugs, high five ...)
:::
* Eating contaminated food (contaminated means it includes uncooked and infected botany produce or has been splashed on / injected with a syringe).
#### Protection
* Can be vaccinated against and surpressed from progressing but not actually be cured. Though supressed its time is still ticking making it possible to not suffer any actualy symptoms.
* Biosuits prevent touch reaction.
* Gloves prevent touching bloody items.
* Masks prevent inhalation.
### Parasites
Multi celled organism that arent infections inside the host until they have reached maturity at which point they either leave the host or start a new cycle.
#### Effect on player
Potentially infinite effect duration with focus on affecting the player more so then the spread itself.

---
## Pathologist
Did the local portal hopping scientist come back looking for brains? Did a sketchy trader offer an absurd amount of money for a bioweapon and you took them up on the offer? The corpse stealing, blood drawing lab goblin is here to deal with all things that have DNA.
### Access
* Pathology lab
* Medbay/Medical equipment
* Morgue
* Maint
### Supervisors
* Medical Director
* Captain
* Head of Security (Cant have a war crime on station without someone knowing about it)
### Responsibilities
* Research pathogens found in space and your fellow crew
* Work on a cure if an outbreak does happens
* Develope pathogens that support the crew
* Turn a profit by categorizing pathogens
* Aid in synthezise of chemicals
### Crew interactions (idealized)

graph LR

subgraph Medbay
Pathologist -- Hands out vaccines</br>and heals --> Medic
end

subgraph Chem production
Pathologist -- provide chems</br>find samples in space --> Scientist
Scientist -. provide chems .-> Pathologist
Scientist -- Supplies Heals --> Medic
end

subgraph Restricted Crates for analysis
QM -- Gets random</br>pathogen Crates --> Pathologist
Pathologist -- Analysis / Creates</br> codes for profit --> QM
QM -- Requests lvl 4</br>crate access --> Medical&nbspDirector
QM -- Requests lvl 5</br>crate access --> Captain/HoS
Medical&nbspDirector --> Pathologist
Captain/HoS --> Pathologist
Mining -- Supplies Crates --> Pathologist
QM -- Sends CDC crates --> Medic
end

subgraph Civilian&nbspinteractions
Pathologist -- Modify Produce</br>and seeds--> Botany
Botany -- Supplier --> Chef
Chef -- Feeds --> Crew
Pathologist -- Cures/infects</br>with pathogens --> Crew
Janitor -- Saves literally</br>everyone --> Crew
end


style Scientist fill:#DF85FF
style Pathologist fill:#B0FFC0
style QM fill:#FFDF8A
style Mining fill:#FFDF8A
style Medical&nbspDirector fill:#FF6365
style Captain/HoS fill:#6DB3FF
style Medic fill:#A8FBFF

#### Medbay
* Treat pathogens that come up
* Supply medbay with potent heals
* Make a supply of vaccines
* Be a source of pathogens
#### QM
* Random analysis crates for profit similar to artlab
* Sends samples to the CDC to requests cures and vaccines
* Gets heads to open crates and sends them to pathology
#### Mining
* Gets pathogen samples from crates
#### Science
* Exchange of chems
* Find pathogen samples in azones/space ~~and mindlessly inject themselfes~~
#### Botany
* Add Pathogens to produce and seeds
* Eventually ends up in the crew when they eat the food
### TODO
Finish crew interactions
### Starting gear
**Shoes**: White shoes
**Gloves**: Blue latex gloves
**ID**: ID
**Uniform**: Pathologist Uniform
**Outer Suit**: Pathology Labcoat (Black or orange biohazard on back)
**Eye**: Medical goggles (get a virus detection overlay)
**Ear**: Medical headset
**Mask**: Emergency gas mask
**Head**: Nothing
**Belt**: Pathologist belt
**Left Pocket**: PDA
**Right Pocket**:
**Backpack**: Pathologist Backpack (Black or orange biohazard on back)
**Left Hand**: Clipboard with analysis form
**Right Hand**: Air tank
**Back**: Pathologist Backpack
#### Backpack:
*
#### Belt:
---
## How to analyze a pathogen
Pathogen analysis works similar to artifact analysis.
1. Start an infection
* Grab a ~~staffie~~ monkey and infect it with your pathogen
* Check the stage the pathogen is currently in and check all the symptoms you can observe.
2. Add the isolated pathogen into the evolution chamber. Add the required chem (determined on a per symptom basis) and hit evolve.
3. Wait until the pathogen amouple is ejected.
4. Get a reward based on the symptom
---
## Fuck I think I've been infected
If there is a method of infection getting to you by methods that dont go straight into the blood and the first stage has any noteable symtoms you will receive a message like,
* "Yuck some of the slime landed on your face"
* "Eating that wasnt a good idea"
* "The hug felt like it was a bit too close"

indicating you have been in contact with a pathogen. These are giveaways for an infected person but not yet a sign that you yourself caught whatever the other person was carrying.
Once the pathogen reaches stage 3 (5 for pathogens) you will get a the status effect "Immune Response" indicating that some pathogen is inside of you.
### Virologist
The pathology lab starts out with a pathogen analyzer which is capable of detecting the majority of/all the pathogens telling you all the information currently available to you based on your research. Alterniatively you can draw some of your blood and **test for a reaction** from your body or residue created by the pathogens.
### Medic staff
You suspect you have been infected and dont remember a suspicious chat message? The health analyzer you start with has a pathogen module capable of detecting if a pathogen is currently inside of you. If for some reason your health analyzer does not come with the pathogen module you can simply buy it from the vendors in medbay. Once a pathogen reached stage 3 and the pathogen causes external symptoms youll be able to detect an infection with the pathogen overlay provided by a pair of medical goggles.
### Average crew
Well you get suspicious text messages? You experience strange behavior like random damage or stuns? Whatever it is you will likely want to head over to medbay to get that checked out. If sufficently far into the disease you will get the "Immune Response" status effect. Which is a dead give away you have been infected. The Minimed vendors sell test kits which will tell you if you have been infected with virii ur bacterias

---
## How to deal with pathogens
### Identify the pathogen
* If the pathogen has been researched or created in pathology, using a health analyzer set to the pathology module on an infected person will show some of the details known already like supressing agents and the maximum number of stages.
* If its an unknown pathogen you can take a blood sample and run it under a microscope. It will generate a name and add a database entry.
* A virologist will get informations on what stage causes what symptoms as well as what can be used to mitigate the effects if applicable.
* Non virologists will only see the way to mitigate the effects of the current stage or how to halt the progression.
* Use the CDC to get an analysis which will send updates with increasingly more details regarding the pathogen, updating the pathogen database in the process.
---
## How to create a pathogen

### Base Pathogen
1. Obtain a data disk
2. Use it on a the pathogen database computer
3. Select the type of pathogen you want to create

### Add a characteristic
1. Browse the already categorized characteristics
2. Select the stage you want the characteristic to occure
3. Hit add

### Synthetize the Pathogen
1. Once you are happy with the pathogen structure hit write.
2. Take the ejected disk and insert it into the Synth-O-Mat
3. Start the process it will take longer based on
* pathogen in increasing order virus -> bacterium -> parasite
* complexity number of characteristics with higher tier ones taking longer
* code repititions. Based on real life issues with DNA synthesis of repeating sequences this should incentivice actually looking at the code and trying to restructure it by just rearranging the characteristics.
4. The Synth-O-Mat will eject a **pathogen ampoule** containing the synthezied pathogen