Guide to Pathology

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Cryo.png Player access to pathology has been suspended pending rework and redevelopement.
Most pathogen sources have been disabled or reworked.
Overalls guy.png This page is under construction.
The following information may be incomplete.
All the info should be correct, but the formatting is terrible.

A pathogen is a disease that can have many different effects. These are combined together by a pathologist, so each pathogen you encounter will likely be unique.

A pathogen is defined by several things:


Suspension of Player Access to Pathogens

In May 2020, the admin team decided to suspend player access to pathology by removing or reworking various sources of pathogens through code and map changes, for a number of reasons explained in this thread. Months later, in 2021, from January 13th to January 20th, it was re-enabled for testing. Pathology still reminds disabled for the most part.

The pathology labs are still there for the most part, though slightly modified, the CDC is still around, all the machines described below are still around, and pathogens still work as described below too, but you just can't get find pathogens as a normal player, barring Admin shenanigans and the odd diseased "burgle" in the Afterlife Bar.

Re-enabling Access

If you want to re-enable player access to pathology to test out your new pathology code or just for your own curiosity, you need to go to _setup.dm in the goonstation/_stdlib/ folder and uncomment //#define CREATE_PATHOGENS 1, so it becomes #define CREATE_PATHOGENS 1. This of course requires downloading and compiling the code, which is explained in the Goonstation Development Guidelines.

Uncommenting the CREATE_PATHOGENS define does the following:

Note it does not reverse the various map changes that came along with the suspension of player access to pathology.

Stats

The Manipulate tab in the Pathogen Manipulator, used to change a pathogens stats.

These are numerical values between 0 and 50 that influence how well the pathogen can do certain things. A pathologist can set these stats directly in the Pathogen Manipulator.

  • Advance Rate: This determines how quickly the pathogen will advance through its Stages. It will also determine how quickly it goes down through the stages when suppressed or in remission.
  • Spread: This determines how well the pathogen will spread from person to person. This also depends on the pathogen's Symptoms. A pathogen with 0 spread will not spread at all by itself.
  • Suppression Threshold: This determines how easily a pathogen can be suppressed via its Suppressant.

A pathogen has only a limited amount of points to spread over these stats, so if it is very good in some stats, the other stats will probably be lower to compensate. The amount of points a pathogen has to spread is known as its Passive Capacity.

Microbody Type

The specific type of pathogen. There are four different types (plus a fifth that only occurs when the admins bombard the station with diseased burgles).

A specific sample has a specific type, and it is unchangeable, so you will need to find a sample with the type you want and then build off of that for your disease.

The microbody type influence a handful of things:

  • Stages: The maximum stage that the pathogen can reach. More on stages later.
  • Active Capacity: This determines how many symptoms (and of what length) the pathogen can support. Adding any more will destroy the pathogen. More on symptoms later.
  • Activity: How often the pathogen can trigger its symptoms. This also differs depending on the pathogens stage.
  • Growth Medium: What type of Growth Medium needs to be added to a petri dish in order for the pathogen to grow. This is a chemical.
  • Anti-Agent: What type of Anti-Agent needs to be used to make a cure in the Synth-O-Matic. This is a chemical.
  • Vaccinable: If a Vaccine can be made for the pathogen.
  • Auto-Immunization: If you are immune to the pathogen after you have been cured of it once.

Here are the different microbody types:

Microbody Stages Activity Active Capacity Growth medium Anti-agent Vaccinable Self-
immunization
Admin-only
Virus 5 1, 5, 20, 30, 40 12 Egg Antiviral Agent Yes Yes No
Parasite 5 50, 40, 30, 20, 10 18 Parasitic Medium Biocide No No No
Bacterium 3 30, 30, 30 25 Bacterial Medium Spaceacillin Yes Yes No
Fungus 1 10 Fungal Medium Biocide Yes No No
Great Mutatis 5 20, 20, 20, 20, 20 Stable Mutagen Mutation Inhibitor No No Yes

For instance, lets say you are infected by a virus. It starts out in stage 1 (as all infections do). While in stage 1, it will only have a 1% chance to trigger it's symptoms, which is very low! But as it progresses through the stages, it will trigger more and more, with up to a 40% chance to possibly trigger symptoms at stage 5.

Something like a Parasite, on the other hand, will start out at 40% in stage 1, so it might spread very quickly! But as it progresses through the stages, it will trigger a bit less (though still a fair amount). This can be helpful for diseases meant to spread quickly, or that have symptoms where it doesn't really matter how much they trigger, because they mainly have passive effects.

A bacterium has a constant activity, so it always triggers at an ok rate, but it can only progress up to stage 3. This means that the symptoms will be a bit weaker, and some really strong effects may never be able to trigger (stuff like gibbing from tier 5 symptoms, for instance). The main advantage of the bacterium though, is that it you can put a lot more symptoms on it than on a virus or parasite, so you might want to go for it if you want a wide variety of effects that are maybe a bit weaker.

Now, you may be thinking, hold on, the fungus is complete garbage! You are correct, the main purpose of a fungus is for it to be used to cultivate lots of symptoms on it, even if you never intend to actually infect anyone with the fungus. You will see what this comes in handy for later, in the section on how to find new symptoms!

Suppressant

The Suppressant, like the microbody type, is an inherent, unchangeable property of a pathogen sample. It is a specific type of stimulus that the pathogen is weak to. When a pathogen is exposed to its suppressant, it might start to regress through its stages, becoming less powerful. Prolonged exposure might even cause it to go into remission, eventually being cured completely. There are a handful of different suppressants, which can be applied in different ways.

You aren't told explicitly what a pathogens suppressant is, it requires a little bit of detective work! Suppressants are split into a few different groups, a quick inspection with a health analyzer or microscope will tell you the group, but not the exact suppressant itself. To find out the precise type, you then simply put a petri dish with a sample of the pathogen under a microscope and use a dropper to drip a little bit of a related chemical into the dish. If the pathogen reacts, you will know that you found the correct suppressant! You can also tell what the suppressant is by the color that the pathogen is when seen under a microscope.

Group Suppressant Trigger Color Associated Chemicals
Thermal Heat Afflicted needs to have a high body temperature Blue Phlogiston, Chlorine Trifluoride
Cold Afflicted needs to have a low body temperature Red Cryostylane, Cryoxadone
Sedative Sedative Afflicted needs to sleep Green Morphine, Ketamine
Muscle Relaxant Afflicted needs to have related chemicals in bloodstream, or receive electric shocks White Haloperidol, Neurotoxin
Medical Brute Medicine Afflicted needs to have related chemicals in bloodstream Black Styptic Powder, Synthflesh
Burn Medicine Afflicted needs to have related chemicals in bloodstream Cyan Silver Sulfadiazine, Synthflesh
Gastronomical Fat Afflicted needs to have related chemicals in bloodstream Orange Partially Hydrogenated Space-Soybean Oil, Space-Soybean Oil, Porktonium, Cholesterol
Chicken Soup Afflicted needs to have related chemicals in bloodstream Pink Chicken Soup
Radioactive Radiation Afflicted needs to be irradiated Viridian Radium, Unstable Mutagen, Uranium, Polonium
Mutagen Afflicted needs to have related chemicals in bloodstream Olive Drab Unstable Mutagen, Stable Mutagen

Suppressants also have a use in manufacturing cures, but these days they aren't really necessary any more.

Symptoms

A virus type pathogen with one tier 2 symptom and three tier 1 symptoms

Symptoms, aka, the fun part of Pathology!
They are what determines what your Pathogen will actually do! Most of the time in creating a Pathogen goes into finding the Symptoms you want. Each Symptom has a unique code that is made of segments. Each segment is a combination of three letters or digits. There are five different tiers of Symptoms, with tier 1 Symptoms being the weakest, but only needing one segment, while tier 5 are the strongest, but are made of five segments.

Everything after the || is the Pathogen's Symptoms! The individual Symptom's codes are separated with |, so as you can see, we have four different Symptoms, one tier 2 Symptom (ffe 001) and three tier 1 Symptom (2e6, ffe, 9dd)!

Examining Symptoms

Now, how do we find out which Symptoms these codes correspond to? For this we will use our good friend, the microscope! Microscope.png

The view visible through the Microscope, after Step 4
The view visible through the Microscope after dripping some Pepper in, after Step 8
  1. Remove your sample from the Pathogen Manipulator and put it into a petri dish. Then put the petri dish into the microscope, so you can inspect it!
  2. Optional: If you think you might take a while to perform these steps, you may want to put some of the appropriate nutrient type into the petri dish as well, or your sample might starve.
  3. Clicking the microscope will then allow you to view the sample in two different ways, either zoomed-out or zoomed-in.
  4. For checking Symptoms, you'll want the zoomed-in view, so click on that one!
  5. The first part of the output in our example (suppressed by something affecting neural activity) shows that the Pathogen's Suppressant is of the sedative variety.
  6. The rest is a bunch of hints, the code next to the hint shows you which Symptom code gave them. Now we just need to figure out what Symptoms these hints are referring to. For this we have a helpful reference guide for the different types of Symptoms! You can find it here!
  7. Now, armed with the knowledge that 'ffe001' is a tier 2 symptom with the hint 'The pathogen appears to generate a high amount of fluids.' we can figure out that it must be either the Sneezing or the Coughing Symptom.
  8. If we wanted to find out which one of the two, we could get ourselves some Pepper from the kitchen and use a Dropper to drip some of it into the petri dish.
  9. We can then observe an addition in the microscope output.
  10. As we can see in the last part, the Sample exhibits the behavior of Sneezing when it interacts with Pepper, so we know that it is Sneezing, and not Coughing! If this seems like a lot of work for one Symptom, don't worry, most of the time you can figure out what a Symptom is without needing to test with Chemicals. Also, you don't always need to figure out exactly what all the smaller Symptoms do, if you are going for big ones anyway!

Finding new Symptoms

Ok, now you may be wondering, all these samples I have contain tier 3 Symptoms at best! What if I want my Pathogen to turn everyone into a pile of ash??
Well, you're going to need to find some bigger Symptoms!

For this, we are going to use the DNA Analyzer function of the Pathogen Manipulator.

The pathogen sample we are splitting. (Before Step 1)
The resulting segments we will receive. (After Step 1)
  1. First, we are going to press the 'Split DNA' button, watch out, this will destroy the currently active Sample in the Pathogen Manipulator!

The destroyed Sample's Symptoms will be broken up into the individual Segments and you will be able to combine the Segments to try to find new Symptom Codes.

Of course, you don't need to do this completely at random! Once you have tested a combination, the lights on the right side will show you some information about that attempt!
If your combination was Stable, that means that it is a valid Symptom that you can put into a Pathogen!
If it was Transient that means that while it is not necessarily Stable, there is another Symptom Code that starts with your combination that is Stable.

The segment '91d' after being tested.

For instance, in our example we start with the segment '91d'. We see that '91d' is both Stable and Transient. This means that we could put '91d' as a Symptom into a Pathogen and it would work! (Which makes sense, since it was already in the Pathogen that we split.) Furthermore, it also tells us that there is at least one other valid Symptom that starts with '91d'. Now, if we look a bit lower, we will see that the Types analysis tells us that there are 2 Good Transient Symptoms and 1 Bad Transient Symptom. Symptoms are split into two categories, Good Symptoms are generally the kind that a person would be happy to have, while Bad Symptoms are usually the ones that harm the Afflicted. The big red lamp on the right side that says "Bad" tells us what kind the symptoms we just tested is.

So, to sum it up, we now know that:

  • '91d' is a valid Symptom. It is of the "Bad" variety.
  • There are three other Symptoms that start with '91d', two of them Good, one of them Bad.

So, naturally, our next step would be to try to add more Segments on to '91d', to see if we can find one of those higher tier Symptoms!

The segment combination '91d 91d' after being tested.

Huzzah! As you can see, this is also a valid Symptom! It is even transient, so there is another Symptom of at least Tier 3 that starts with '91d 91d'.
We also now know that '91d 91d' is a Good Symptom, which might be nice if we are a non-traitor pathologist.
If we check the Pathogen Symptoms & Mutations page, we see that it must be one of the following:

  • Detoxication
  • Oxygen Farts
  • Wound Mending
  • Burn Healing


On the other hand, if you are a traitorous pathologist, you may wish to instead try more combinations that start with '91d 91d' in order to find the higher tier symptom that is harmful.

There are always 6 different Segments in each round, but you can see that the pathogen we split only had 4 different Segments. (91d, a62, df6, f10)
This means that I may not necessarily be able to find this higher tier Symptom with the Segments I have available, because what if the combination I need is something like '91d 91d aca'?
For this reason it is usually a good idea to first make a Fungus with every kind of Segment (and lots of them, so you can use them to combine more often before having to load in a new sample).

Splicing Pathogens

Alright, so how do we make a testing pathogen for finding new combinations? And how do we put the combinations we find into an actual pathogen?
Well, for this we will be using the Splicing system!
First of all, we should get ourselves plenty of different samples. This can be done at the Synth-O-Matic! Synth-O-Matic.png
For making a testing pathogen, Fungus is a good choice, since it can support an infinite amount of Segments. Other microbodies will collapse if you try to Splice too many Symptoms onto them! (See Section on Microbodies)

Once you have your Samples, just put them all into the Pathogen Manipulator by clicking. It can hold up to 4 at a time. (Counting the currently active Sample.)
SplicePatho1.PNG
Next, simply click a SPLICE button to start splicing the active Sample together with the Sample whose SPLICE button you clicked.
SplicePatho2.PNG
Now you can splice any Symptom Segments you want from the bottom Sample into the top Sample with the Before and After buttons.
The Remove button can be used to remove any Segments you do not want.
The + and - buttons let you change the size of your selection, so you can transfer more than one Segment at once.
Remember that all the Symptoms (the stuff between the |s) in the top Sample will need to be valid Symptoms, or the Sequence will collapse and the Sample will be lost!
The Sequence will also collapse if the amount of Symptom Segments exceeds the Microbodies' Active Capacity. (as mentioned in the section on Microbodies).
Another tip: the part before the || is the Suppressant code, do not modify it, and do not attempt to put the one from the bottom into the top sample. There is no point and it'll probably mess up your Sample.
(In this case that would be f2d.)
Here is what we end up with in this case:
SplicePatho3.PNG
Once you are done, click the Finish Splice button.
Now we do this for all the other Samples too, and end up with a really long supersample, which we can use to experiment and find new Symptom Codes!
SplicePatho4.PNG

Growing more Pathogen

Of course, using the DNA Analyzer on a Sample will destroy the Sample, and we wouldn't want to use up the Sample we just put so much work into, right? That is why we simply make it grow to obtain more Samples that are exactly the same as our initial one!

  1. Put the sample from the vial into a petri dish.
  2. Add some nutrients to the petri dish, of the appropriate type for the microbody. The table for this can be found here.
  3. Wait a minute or two until the pathogen starts to grow.
  4. Transfer pathogen from the dish into vials, making sure to keep some in the dish so it can continue to multiply.

A sample needs to have at least 2 units of pathogen (a mechanical dropper can be used to transfer exactly 2 units). All you need to watch out for is the pathogen running out of nutrients and not to remove the last bit of pathogen from the petri dish. You can also use the Incubator, it will automatically keep one petri dish supplied with nutrients, and you can use a vial on it to fill it with pathogen (if there is enough in the petri dish). If you are familiar with a reagent heater, the Incubator looks exactly the same. ChemHeater.png

Handling Infections

Alright, you've found a bunch of Symptoms, put them on the kind of Microbody you want and adjusted the Stats to your liking! Now what?
Well, infecting someone is very easy! Simply inject the pathogen into their bloodstream and they will be infected with it. This also works with blood extracted from an afflicted person.
Splashing it on them can also work, but it depends on their disease resistance, which is mainly modified by their clothing. Naturally, a biosuit/hood or a spacesuit/helmet combo will protect against any diseases splashed onto a person.

Assuming that your pathogen has one or more spreading Symptoms (coughing, sneezing, farting, hugging, etc...) and a Spread Stat that is not 0, it will also be able to spread itself! How exactly this goes down depends on the Symptom in question, you can read up on this on the Pathogen Symptoms & Mutations page.
One important thing to remember is that some Symptoms make disease clouds. If you are not breathing from and air tank you will breathe these in, rendering your protective suit useless, so make sure to use internals!

It is worth noting that unlike in real life, a person can be afflicted with only one pathogen at a time. Someone already infected can only get a new infection if they are exposed to a pathogen with at least one symptom that is higher in tier than the highest tier symptom in the existing pathogen, in which case the new disease "overwrites" the prevoius one. For example, say you're afflicted with a pathogen whose highest tier symptom is Oxygen Farts, tier 2 symptom. You can't get infected by a pathogen whose highest tier symptom is Snapping, another tier 2 symptom, but you can be infected by one with Projectile Bee Egg Sneezing, a tier 3 symptom, in which case you lose the pathogen with Oxygen Farts but gain the one with Projectile Bee Egg Sneezing.

Curing Disease

Oh no, there is a horrible disease going around the station and for some reason it is your duty to cure it! Don't worry, there are several ways you can accomplish this, and most of them are pretty simple.

QM

Do you have Cargo access? Do you really not want to bother with pathology? Then this is the way for you!
Simply go to the Cargo Console and use the Contact CDC button.
CuringPatho1.PNG
Then requisition a Biohazard Material Crate from them.
CuringPatho2.PNG
Shortly after the crate will arrive, just like any other kind of QM crate.
Now just put a sample of the pathogen into the crate and send it back out, as if you were selling something. The easiest way to do this is to just take blood from an infected person. The CDC even send an empty syringe in the crate for just that purpose!
CuringPatho3.PNG
Shortly after the CDC should be ready to start analysis on the sample you sent, simply click on analyze some samples and then click on the sample you want analyzed. Presumably there will be only one, it's pretty rare that several samples get sent to the CDC in a round!
CuringPatho4.PNG
They analyze the sample pretty much instantly, once that has happened you can simply order batches of cures from them that will then arrive shortly after, just like regular QM orders.
Each batch contains several cures, simply stab an infected person with one of these, and their pathogen will go into remission. It will then slowly go down through the stages and cure itself once it is done.

Cure Manufacturing

Do you like doing things the proper way? Did the traitor pathologist not blow up the lab after they were done? Then this is the correct way for you!

The Synth-O-Matic UI, which can be used to synthesize cures.
  1. Take a blood sample from an infected person using a syringe.
  2. Inject the blood into a blood slide. There are some around the lab and in the path-o-matic vendor.
  3. Put the blood slide into a microscope and check what kind of Microbody you are dealing with. You will need to know this to figure out the appropriate anti-agent. You can check these in the table here.
  4. Put the blood slide and a clean petri dish into a centrifuge and start it. Centrifuge.png
  5. After a short time, you should have a proper pathogen sample inside the petri dish. Take it out of the machine.
  6. Give it nutrient to grow more of it as outlined in the Pathogen Growing section.
  7. Put some of the samples from this into vials and put the vials into the Synth-O-Matic. Synth-O-Matic.png
  8. Add some of the appropriate anti-agent from the Path-O-Matic vendor and pick the anti-agent option when putting it in. Don't worry about the suppressant option, it is not necessary right now.
  9. Once both things are in the Synth-O-Matic, simply click the vial in the list of inserted vials and then select the Synthesize serum by irradiation option.
  10. After a second or two, the machine should spit out some cures. If you did everything correctly, stabbing one of these into someone should put the infection into remission. (If you did not, they will instead infect people.)

Curing via Suppression

Do you not have access to QM or a Pathology Lab? Do you not want to do any fancy science stuff? Then this is the section for you.
Figure out the Suppressant as described in the section on Suppressants up above. Then expose yourself to it until your Pathogen goes into remission. It's that simple!
A humble health analyzer will tell you the Suppressant Group of the disease. From then you really only have two different options that you need to try. You'll know you have the right Suppressant if you get a message about feeling better, or if the Stage of your Infection (as seen on the health analyzer) decreases.

Supplementary Video

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Medsci Doctoring · Genetics · Guide to Pathology · Pathogen Symptoms · Robotics · Telescience · Plasma Research · Artifact Research · Chemistry · Chemicals · ChemiCompiler
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Computers Computers · TermOS · ThinkDOS · Packets