Pathology Research (old)

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Pathology Research is a branch of medical science where the study, curing, manipulation and perhaps manufacturing of pathogens happens. In this area you will find a large set of unique tools that allow you to conduct hellish experiments on tiny, questionably-alive organisms.

The base concepts of Pathology

A pathogen is a structure with multiple different types of components on one body. Unlike in the old pathology system, where a disease is well-defined and has a specific way it plays out, a pathogen is a composition of different, smaller effects, creating a possibility for infinite different diseases.

Microbody

The microscopic body is the base, bare-bones structural element of a pathogen. Each pathogen is a microbody of sorts, and this microbody determines the initial value of its attributes and the level of activity the pathogen manifests on each stage of infection. The microbody also determines the type of anti-agent that should be used for cure synthesis. Infections from all bodies can be cured, but vaccines, which prevent infections, can only be manufactured for some of them. Different microbodies can be cultivated under different circumstances. Cultivation requires a growth medium and nutrition specific to that body.

Microbody	Vaccine	Anti-agent	Growth medium	Nutrition	Initial stages	Activity
Virus	Yes	Antiviral Agent	Egg	Iron, Nitrogen, Sodium, Sugar, Water	5	Low to high
Bacterium	No	Spaceacillin	Bacterial Medium	Iron, Nitrogen, Sodium, Sugar, Water	3	Low to high
Fungus	No	Biocide	Fungal Medium	Iron, Nitrogen, Sodium, Sugar, Water	4	Near constant
Parasite	No	Biocide	Parasitic Medium	Iron, Nitrogen, Sodium, Sugar, Water	5	High to low
Great Mutatis cell	No	Mutation Inhibitor	Stable Mutagen	Stable Mutagen	5	Constant

Suppressant

All pathogens have an inherent weakness, which needs to be discovered in order to create cures. This weakness is manifested when coming into contact with an appropriate suppression agent. A suppression agent for a pathogen is one of a group of reagents exhibiting a specific trait - such as hot reagents (ClF3 or phlogiston), cold reagents (cryostylane) or brute medicine (synthflesh, omnizine). In order to test this, a pathogen sample must be introduced to the reagent while being observed under a microscope. Simply add a few units of the pathogen reagent to a petri dish, then place the petri dish on the microscope. Then, use a dropper on the microscope to introduce a small amount of the reagent to the culture, finally, view the petri dish through the microscope in both a zoomed in and zoomed out state. A message about a reagent weakening or negatively affecting the pathogen culture is a good indication of that reagent acting as a suppressant.

The suppressant is not only a reagent that is used for cure synthesis, but also a reagent that will slow down the worsening of an infected individual's symptoms. Thus if you require time to cure everyone that's been infected, injecting them with a high amount of the appropriate suppressing agent is likely to keep them alive longer. Unless, of course, the suppressing agent is something that is inherently harmful. The amount of suppressant reagent required to keep the patient relatively stable is determined by the suppression threshold of the pathogen.

The suppressant inherently determines the color of the pathogen. Be careful, though, as multiple different suppressants might have the same color!

Each suppressant has a DNA signature consisting of three hexadecimal digits (such as F0A). The DNA signature is usually different than that of any symptom, and thus is rarely useful in symptom splicing.

Symptom

A symptom of a pathogen is a trait exerted when infecting a human. Symptoms can be something fairly innocent, such as constant moaning or reciting Shakespeare, or something deadly, such as spontaneous combustion or gibbing. A pathogen may have any number of symptoms, though initial unmutated strains usually have 1 to 5 different symptoms on them.

Symptoms may also be positive instead of negative - such as wound mending, or detoxicating. The aim for a non-traitor pathologist while not busy curing infected individuals should be to create a beneficial pathogen.

Pathogens have a varying amount of stages, the stage being a values that determines the potency of symptoms. Thus a pathogen with 3 stages and a gibbing symptom will never gib infected individuals, as a gibbing event may only occur in stage 5. Mind the amount of stages a pathogen has - it is a value that can be determined from a glance at the private DNA of the pathogen.

There are 5 tiers of symptoms present in the game. Higher tier symptoms are increasingly rare, however, they can be synthesized artificially through splicing. More on this subject below.

The secondary function of symptoms is transmission of the pathogen between individuals. A pathogen that has no symptom creating a forced ejection of bodily fluids (such as coughing, sneezing or sweating) is unlikely to be contageous. A station-wide contagion can only happen if a pathogen has one or more of these symptoms.

Mutation

Initially, each pathogen is assigned a number of properties, however, this is subject to change over time. Pathogens mutate and adapt according to their attributes. There are several things which may induce a mutation on a pathogen, such as:

Infection. When an individual becomes infected with a pathogen, there is a probability, depending on the mutativeness of the pathogen, that the newly infected individual will be infected by a mutated version of the pathogen.
Radiation. A pathogen irradiated in the pathogen manipulator has a chance to mutate, and pathogens residing in irradiated individuals may also mutate over time.
Mutagenic symptoms. Certain symptoms might cause their base pathogen to mutate.

A strain of pathogen is assigned a base name with the pattern LNL, where L is an arbitrary letter, and N is a number 1-99. This is the base name of the pathogen, which will be used to identify it. Any pathogen with the same base name can be cured with a cure created using any other pathogen with the same base name. A pathogen strain with the same base name will always share the same microbody, but may have a different suppressant due to splicing. The specific mutation of a pathogen is identified by the last number, appended after the base name. For example, A1B2 and A1B3 have the same base name (A1B) and thus are considered the same pathogen, but may have different symptoms or attributes due to the different mutation number (2 and 3 respectively).

The frequency and nature of the mutations occurring are affected by a number of pathogen attributes.

TODO: A table listing possible mutations.

Attributes

Attributes are numeric values of the pathogen. There are two groups of attributes: primary attributes, which can be affected by the pathogen manipulator via the manipulate option, and secondary attributes, which can only be modified through mutation.

The primary attributes specific to a pathogen:

Advance speed determines how quickly a pathogen advances to its final stage. A very high advance speed is likely to cause a pathogen to hit stage 5 in a matter of minutes, while a negative advance speed might cause an infection to cure itself.
Maliciousness determines the nature of mutations occurring on a pathogen. A high maliciousness value will enable very bad things to happen when a pathogen mutates (such as gaining multiple additional bad symptoms), while a negative maliciousness value will promote the occurrence of benevolent mutations (such as losing a bad symptom).
Mutativeness is initially determined by the microbody of the pathogen. Virii and great mutatis cells are very mutative, while fungi are unlikely to mutate over time. Mutativeness translates to a flat chance of mutations occurring on a pathogen on infection. A negative mutativeness will also induce mutations, albeit devolutionary ones.
Mutation speed determines how many mutations will occur if a mutation happens. Mutation speed is a logarithmic scale, thus you need increasingly higher values of mutation speed for that one extra mutation to happen. For example, at a mutation speed of 10, chances are that if the pathogen mutates, two different types of mutations will happen to the pathogen.
Suppression threshold is a value which is primarily used in cure synthesis. The threshold determines the minimum amount of reagents required to suppress a pathogen while infecting an individual, and also determines the minimum amount of suppressant reagent and anti-agent required in the Synth-O-Matic for synthesizing a working cure or vaccine.

The secondary attributes specific to a pathogen:

Stages is the maximum severity of this pathogen. The amount of stages on a pathogen will always be between 3 and 5. The mutation causing the stages to decrease is a devolution, and will not occur on positive value pathogens. The amount of stages is initially determined by the microbody.
Generation determines the priority of a pathogen. An individual may only be affected by a single mutation of a pathogen strain at a time (and thus cannot be infected with both A1B2 and A1B3 simultaneously). A higher generation number pathogen will always assimilate a lower generation pathogen, thus if someone infected with A1B2 is introduced to A1B3, and A1B3 has a greater generation number, the individual will instead be infected with A1B3 from there on, continuing from the same infection stage. Mutations might cause this number to increase, but never to decrease. A gene-modified pathogen will always be generation 1 when removed from the Pathogen Manipulator.
Symptomaticity is a flat boolean, which determines if symptoms are exerted on an individual. A mutation might cause a symptomatic pathogen to become asymptomatic and vice versa. Note that an asymptomatic pathogen is not completely inert - contageous symptoms, such as coughing, will still be active on asymptomatic infections, but purely non-contageous symptoms, such as spontaneous combustion, will not occur.

The tools at your disposal

Your laboratory consists of a number of tools, each of which you must be familiar with to be a successful pathologist.

Blood Slide

Blood slides are where it all begins. These items will store blood samples extracted from a person. Blood samples function like pathogen samples in an inferior way. They can be examined under the microscope, but cannot be reacted with reagents. They cannot be used for cure manufacturing, cultivation or manipulation. To do this, a singular pathogen sample must be isolated out of the blood slide using the...

Centrifuge

The centrifuge is a large machine that given time will extract a pathogen sample from a blood slide into a petri dish. This extraction will always yield 5 units of pathogen sample, and it will destroy the blood slide. Please note that out of a single blood slide only a single pathogen can be isolated - even if it contains multiple different ones.

Petri Dish

Now that you have extracted your pathogen sample, it should be in a petri dish. Petri dishes are special appliances that can be used to cultivate a pathogen. Pathogen cultivation requires two different things:

A medium used to coat the petri dish.
A couple of nutrients to keep the pathogen well fed.

Each microbody has its own medium and growth nutrients. To initiate cultivation, simply add a pathogen to the petri dish, add the medium and a sizeable amount of all the nutrients and wait. In a few minutes, the amount of pathogen will begin gradually increasing in the petri dish. Note that you need a least a single unit of pathogen in the petri dish at all times otherwise the cultivation will stop!

When the dish runs out of nutrients, the cultivation process goes into reverse. Once the reverse process reaches its end-point, the pathogen in the dish will begin slowly disappearing - dying.

If a petri dish is misused, it will become dirty. A dirty petri dish cannot be used for pathogen cultivation. Examining a petri dish will tell you if it's dirty or not, and inspecting a dirty petri dish under a microscope will tell you why the petri dish became unusable. To be able to re-use a dirty petri dish, you need to clean it in the...

Autoclave

A large machinery which will remove all traces of reagents from a glass container. This includes cleaning a petri dish thoroughly enough to be able to use it for pathogen cultivation once again. To do this, simply slap the petri dish in there and activate the machine. After a sizeable amount of time, it will eject the once again useable petri dish.

Microscope

The microscope is the most important research tool in Pathology. Using this and a wide array of reagents, you can discover what features a pathogen holds - without this, you are completely blind.

Microscopes can observe blood samples in blood slides and pathogen samples in petri dishes. The latter is the recommended way of observation, as the blood slides cannot be used with reagent reactions.

To use the microscope, use the appropriate receptacle on it, then use the microscope with an empty hand. The microscope has two zoom states: zoomed in and zoomed out.

While zoomed out, you will see:

A vague description of the pathogen (eg. red chunky viruses). This holds key information for cure manufacturing: the type of the microbody, and the color, which is a hint at the suppressant.
Any reactions to a chemical that affect the pathogen culture as a whole.

While zoomed in, you will see:

Finer features of the pathogen, which hint at either a symptom, a suppressant, or a reagent to use to get a hint at a symptom or a suppressant.
Any reactions that affect individual pathogens.

Using the hints that don't hint at a reagent, you can already probably discern a few symptoms the pathogen might exert. To discover the rest, especially the suppressant, use a dropper filled with any reagent on the microscope while a petri dish is under the microscope, then view the pathogen in both a zoomed-in and a zoomed-out state. If the pathogen reacts to the reagent (due to a symptom, or perhaps the suppressant), you will see messages you did not see before.

When creating cures, the key function of the microscope is to determine a reagent that suppresses the pathogen. Using the hints, this should be a relatively easy task. If you are sure that you have found the right suppressant, you are ready to make a cure using the...

Synth-O-Matic

A truly mystic machine, the synth-o-matic will take a vial of any pathogen and two beakers and output one or multiple syringes of possibly a pathogen cure. To use the machine, insert a vial of a pathogen sample into it, then select it on the machine interface. Depending on the type of synth-o-matic modules you have in the machine, you may get additional helpful information. You may acquire these modules from various traders or the QM office.

When synthesizing a cure, along with the clean pathogen sample, you will require:

A beaker of anti-agent, greater in amount than the suppression threshold of the pathogen inserted. The anti-agent is specific to the microbody. Be sure to ration the minimal amount of anti-agent your lab starts with, otherwise you will need to ask some scientists to make you more!
A beaker of a suppressing reagent. The method for discovering the suppressant is detailed above. Again, you will require an amount greater than the suppression threshold of the pathogen, otherwise the cure will be faulty.

With the synth-o-matic modules, you have a number of additional options:

The synthesizer module allows the Synth-O-Matic to create anti-agents, thus easing your reliance on chemistry.
The irradiation module relieves your need to rely on suppressing reagents, replacing the suppressant with radiation. It takes a longer time to manufacture syringes with radiation.
The upgrade module increases the efficiency of the machine, creating four syringes at once instead of one.
The assistant module is a module is capable of analyzing and determining the suppressant of the pathogen. It will suggest the appropriate suppressants and also the minimal amount of them required.
The vaccine module allows the creation of vaccines for vaccinable microbodies. Vaccines do not require anti-agents, only suppressants. You can create vaccines only using radiation, as well. Note that a vaccine may also be faulty when created improperly!
The microbody modules are a set of modules that allow you to create the cures. All microbody modules are initially loaded into the Synth-O-Matic machine, other than fungi, which must be acquired separately. Make sure these aren't removed! If you lose them, Cargo Bay can order replacement modules.

Synthesize your cure with the appropriate options, and the machine will spit out one (or more) syringes after bubbling a bit. Be careful! If you messed up with the anti-agent or the suppressant, the cure will not put anyone's condition into remission, and will infect anyone that's not already infected! You cannot visually differentiate between working and faulty cures, thus simian testing is encouraged before human testing.

Pathogen Manipulator

Now that you are an experienced healer of infections, the time has come to create your own. You open up this machine and OH JESUS CHRIST IT'S NUMBERS AND LETTERS AND VERTICAL BARS WHAT DO I DO?

First, it's important to understand what the pathogen DNA looks like. Here is an example of a pathogen DNA: 000100130006FFFA00070005510C3||1F3|EE2|1F3EE2

The DNA has two parts: a private part, that contains the attributes of a pathogen and a public part, which represents the suppressant and symptoms.

The private part cannot be spliced, its individual elements, however, can be manipulated by irradiation. Manipulating the primary attributes of the pathogen can be done using the Manipulate option in the manipulator. Each attribute can be nudged upwards, or downwards, which will cause movement in the opposite direction on some other attributes. The private part of the pathogen is the first 26 hexadecimal digits of the pathogen DNA, in our example: 00010013000600050007000551. Decoding this:

The first four digits represent the unique identifier of a pathogen microbody. In our case, this is 0001, which is a virus.
The next four digits represent the mutativeness of the pathogen in one's complement. In the example, this is 0013, which is 19 in base 10.
The next four digits represent the mutation speed of the pathogen in one's complement. In the example, this is 0006, which is 6 in base 10.
The next four digits represent the advance speed of the pathogen in one's complement. In the example, this is FFFA, which is -5 in base 10.
The next four digits represent the maliciousness of the pathogen in one's complement. In the example, this is 0007, which is 7 in base 10.
The next four digits represent the suppression threshold of the pathogen in one's complement. In the example, this is 0005, which is 5 in base 10.
The next single digit represents the amount of stages of a pathogen, which can be anything 3-5. In our case, this is 5.
The next single digit represents the symptomaticity of the pathogen. In this case, this is 1 (symptomatic).

One's complement is a binary representation of numbers. In our case, all one's complement numbers are 4 hexadecimal digits long, which equate to 16 bits. In this representation, the leftmost bit represents the sign of the number (- if 1, + if 0). If the number is positive, the other 15 bits represent the magnitude of the number, and if a number is negative, then the magnitude of the number is the complement other 15 bits. This means that 1 would be represented as 0001 (0000 0000 0000 0001 in binary), while -1 would be represented as FFFE (1111 1111 1111 1110 in binary). FFFF and 0000 both mean 0, the machine will however always represent 0 as 0000.

The public part can only be modified by splicing the pathogen with different pathogens. Before we get into splicing, let's take a look at the public part's structure - in our example: 0C3||1F3|EE2|1F3EE2. Decoding this:

The first three digits will always represent the suppressant. Each suppressant has a unique three digit identifier incompatible with any symptom identifiers. In our case this is 0C3, which represents some suppressant. The suppressant codes are round-randomized, thus a suppressant will always have the same code on all pathogens during a single round, but will change between rounds.
The suppressant is followed by two separator enzymes, which must be present after the suppressant.
This is followed by a list of symptoms the pathogen exhibits. Each symptom has a round-randomized code that is of a length divisible by 3, up to 15 digits.

Symptom codes are assigned by tier the following way:

The lowest tier symptoms (tier 1) are assigned a three digit code. All three digit groups found in the effect list of the DNA represent a valid tier 1 symptom.
For each higher tier, the symptoms are assigned a code by taking the code of a symptom from a lower tier (so in case of tier 2, taking the code of a valid tier 1 symptom), and are either appended the code of a tier 1 symptom, creating a code that is 3 digits longer than the code of a symptom a tier below.

An example of the code creation behaviour:

Let's assume tier 1 symptom A gets the code 111, and tier 1 symptom B gets the code 222.
A tier 2 (C) symptom will pick any tier 1 symptom (in our case, either A or B), and a tier 1 symptom (again, either A or B) and create the code. Thus the possible codes for this tier 2 symptom are: 111 111, 111 222, 222 111, 222 222. Let's assume this symptom got the code 222 111
A tier 3 symptom will pick any tier 2 symptom (C in this case) and any tier 1 symptom (either A or B) and create the code. Thus the possible codes for this tier 3 symptom are: 111 222 111, 222 111 111, 222 222 111, 222 111 222.
And so on!

The combinations are also round-randomized, thus if you want to create something really deadly, you must discover how to create it in that round.

Now, on to splicing. Splicing takes a target and a source DNA. The target DNA will be the one we modify, and the one that's loaded into the manipulator. Upon splicing you will be asked to choose a source DNA. Then, the splicing commences. In splicing, select a segment on the target DNA and on the source DNA. Then, you have three actions: Delete the currently selected target DNA section, add the selected source DNA section after the selected target DNA section or add the selected source DNA section before the selected target DNA section.

Once you finish the splicing, the manipulator will attempt to assemble the pathogen with the newly created DNA. If the DNA is imperfect, for example, an invalid symptom is specified in the DNA (going by the above example, 111 222 does not exist, and thus is an invalid symptom), the DNA will collapse and be lost. It is important to cultivate the newly created pathogen after each successful splicing, or you might risk losing it altogether!