6 ms·

How can a software developer contribute to cancer reasearch/treatment? Is there any hard problems? or manual work that could be automated?

by z3t4 7y ago

thanatosmin 7y ago
There are many hard problems and some that can be addressed by algorithms/automation. I think the best advice I can give is reaching out to a lab in your area that does cancer research. Most are happy to talk about what hurdles exist. We, for example, don't have the one true solution to cancer, but a whole lot of computational and algorithm needs that will improve our understanding of the disease.
jaimex2 7y ago
Well, they are tackling the problem medically. Why don't we try and engineer around the problem. All cancers exist for the same reason - our immune system isn't picking them up. Ideas? 1. Nano bots to replace immune system 2. Blood monitoring kits like Theranos tried. 3. Inmune system training kit that tries to encourage attacking cancer cells ( huge backfire potential ) (Disclaimer - I have no idea what I'm talking about )
- abhikshah 7y ago
  Your intuition here is great. 1. Nano bots -- no idea; outside my wheelhouse. 2. Liquid Biopsy -- many companies are working on diagnostic tests to detect cancer early, monitor treatment, detect recurrence, etc. Some of these products are already available but most are in R&D phase. 3. Immuno-Oncology -- the most promising development in cancer treatment in a long time. Successful tumors evade the immune system by essentially hiding themselves. Many companies are working on treatments to assist immune system in different ways. Some products have been in the market for a while now and have been pretty successful.
  - rayhendricks 7y ago
    There is tremendous potential in Immuno-Oncology. I worked with umbilical cord blood [hematopoietic stem cell] transplants and this area really has tremendous potential for tech that only started being used in the late 80s to 90s. IMO much of the immediate potential for progress in software development will be with the legal and ux itself of ten tech though. Apart from a few companies the software is old, buggy, and has not or will be very slowly updated. One idea that comes to mind is making vastly improved LIMS and electronic patient recodkeeping software, as what is presently being used [bbcs] is from the 80s although this could be accomplished with just a front end written for it.
tejtm 7y ago
Work for Universities (for P.I.s housed at universities) for less than you are worth on the open market. (And still be resented by profs making less) Soylent data (it is made of people), is hard because it has all these lawyers attached to it. Figure out a trivial/foolproof way for EHRs to be satisfactorily anonymous for the legal departments to allow sharing but still be useful. (I won't be holding my breath) A concrete thing without any "hard" bits There is an open source tool named Protege that is ... err... the best tool of its class ... fix it or make a replacement []https://protege.stanford.edu/ https://protege.stanford.edu/
- optymizer 7y ago
  I worked for 5+ years for a PI at a prestigious institution. Overall my experience there was great. It was a lot of fun too. I got to design and implement fairly large projects early on as a junior engineer. I could use any tech that I wanted. I had maybe two dozen users at best, but I interacted with them weekly if not daily. That said, I was barely making 50k. Now I'm a senior engineer at a FAANG and though I am more financially stable, I am not having as much fun. I routinely push code to millions of users now, but I don't see any of them. I suppose the FAANG is a different kind of fun, but sometimes I just miss being the guy who's coding this awesome tool that's going to further scientific research, and your post reminded me of that. Maybe when I retire I'll go back to help some PIs with their software issues. I know they need the help.
  - iandanforth 7y ago
    To put you on the spot. It would be great if "maybe when I retire ..." was an actual plan you had. It sounds like you have the opportunity and ability to personally make a difference, I sincerely hope you do. :)
    - optymizer 7y ago
      Thanks for the vote of confidence. I think it's early to make concrete plans though. I have a few other ideas to try out before I turn to academic research.
gww 7y ago
There is a lot of data being produced in these studies and outside of them. There are so many areas that a software developer could really benefit these projects. For example, a lot of bioinformatic software that is released is designed poorly, non-functional or hard to adopt. I wish there was a better way to integrate bioinformatics research with better software development principles. Unfortunately, there isn't a lot of motivation to make good software as the end-goal in most cases is to just get a publication and move on. There are examples of groups that really do put a lot of effort into quality software such as Seurat [1] or scanpy. Another area is trying to manage and process the datasets in large studies -- especially meta studies. Even for some of my small projects I dedicate a huge amount of time trying to curate random tables from publications, convert gene identifiers etc. [1] https://satijalab.org/seurat/ https://satijalab.org/seurat/ [2] https://icb-scanpy.readthedocs-hosted.com/en/stable/ https://icb-scanpy.readthedocs-hosted.com/en/stable/
Aperocky 7y ago
I would think there’s a lot, especially with molecular biology taking a computational twist.
chriskanan 7y ago
I work at a start-up (Paige) working on creating an AI-powered software platform for improving cancer diagnosis and treatment. We have a bunch of job openings (both AI and non-AI) and have raised over $70M. There are a handful of other companies out there working in this space, but there is a ton of opportunity for software developers to contribute. Feel free to email me (see profile) if you would like to talk about it.
whoisterencelee 7y ago
Take a look at boinc there are many cancer related computation projects
asdff 7y ago
Read up on the state of the bioinformatics field and get a feel for the tooling used in typical pipelines. There will be a lot of R and high performance computing. There's no shortage of work to be done.
TristanDaCunha 7y ago
If you make a lot of money, almost certainly the best thing you can do is earning to give¹. Your impact would be far greater again if you were to donate towards any cause other than one which mostly victimises wealthy people.² Instead of cancer victims, you could help poverty victims or animals in factory farms. ¹https://80000hours.org/articles/earning-to-give/#should-you-earn-to-give https://80000hours.org/articles/earning-to-give/#should-you-... ²https://www.effectivealtruism.org/articles/introduction-to-effective-altruism/ https://www.effectivealtruism.org/articles/introduction-to-e...
- rmtech 7y ago
  That's not an answer to the question that was asked. Some people might not want to help animals or people in the third world, they might specifically want to help cancer patients. Furthermore if someone is looking for the most important thing to work on, it almost certainly isn't animals or third world poverty, though it also probably isn't cancer either (unless they have an unusually efficient way to help), because cancer is basically the least neglected cause in the world, as well as being highly intractable. If you want something a lot more impactful than working on either of these things you have to think outside the box, do something that few others are working on and that could have a large impact in a way that is not well-known.
  - gus_massa 7y ago
    > as well as being highly intractable. It varies a lot with the type of cancer, how fast it grows, how advanced it is, and a thousand of additional factors. https://en.wikipedia.org/wiki/Cancer_survival_rates https://en.wikipedia.org/wiki/Cancer_survival_rates Cancer is not a single illness, but a family of related illnesses, the main problem is that we don't have a different street name for each one. Imagine viral infections. What is the survival rate for viral infections? It can be a common cold, or Ebola, or somethin in between.
    - rmtech 7y ago
      Cancer is a group of illnesses that share a key common trait of uncontrollably dividing cells. But when I say intractable I mean that the amount of output in lives you get per dollar of input is small compared to other issues that you can help with.
DrScientist 7y ago
Lot's of ways - just look at the job pages of Cancer institutes/hospitals, Universities and research institutes or biotech/pharma companies. There is a huge amount of scientific and clinical data to make sense of - a lot of it in the public domain. Understanding the mutations at the molecular level is only a start - if you want to treat then you will likely need to understand how that mutation manifests into biology - what processes are affected and there you get into the very complex networks that is biology. But if you don't have a science background, it doesn't matter as most of the actual work is data management, processing and wrangling, before you can get to the insight bit. A lot of the data is being generated a huge scale as well - so making some of the existing analysis fast is also needed. A lot of the scientific software in the bioinformatics area can be found on github - so there it's as accessible to collaboration as any other github project.
- probably_wrong 7y ago
  > Lot's of ways - just look at the job pages of Cancer institutes/hospitals, Universities and research institutes or biotech/pharma companies. I'd be slightly weary of putting "pharma companies" in the same list, or at least not without the following warning: Pharma companies are still companies. That means: research will be often killed because it's not in the company's financial interest to pursue it further: if your drug is better but the market for it is small, your drug won't make it. It is not unheard for a company's plan for cancer to be "we'll wait until someone else does it and then we'll buy them". Pharma companies still fund their own research, and they are still putting out new, more effective drugs in the market. They probably pay better, too. But if you're making a career change because you're idealistic about "making the world a better place", a pharma company might not be the best move.
  - natechols 7y ago
    > if your drug is better but the market for it is small, your drug won't make it As written, this is not what actually happens. The only way to know if a drug is "better" is to run expensive (and risky) clinical trials on it. Big Pharma wouldn't even bother going that far if the market isn't sufficient to make a profit - given the extremely high rate of failure in clinical trials, they never would have started the program in the first place. I realize this may seem like a minor semantic quibble but there is an awful lot of disinformation like "Big Pharma could cure cancer but it's not profitable" floating around.
ankitvgupta 7y ago
Cancer therapeutics development effectively boils down to a massive-scale optimization problem over a highly multi-dimensional surface. The status quo in the industry is to say "let's find a sufficiently good local optimum by having humans largely-manually try to make transformations to known molecules" in this space. But with software, we can address this issue way more systematically. Here are some questions we can ask (and answer with software) to drive this process more rationally: * How might you represent the molecules that define this space? (lots of graph theory, linear algebra, vector math) * How would you model their biochemical properties? (w00t supervised machine learning, but also physics simulations) * Once you build a model for a properties, how can you deploy that model at billion-scale to start searching this space? (containerization, distributed systems, k8s) * How do you iteratively improve your compounds (generative machine learning, evolutionary optimization, lots of search/RL methods) * Once you choose a compound you like and get some experimental data about it, how does that new ground truth value change your model? (data warehousing, data pipelining) * If that data is valuable, how do you keep it safe? (network security, ACLs, virtual private cloud configurations, VPNs, etc.) * How can we visualize what our data and predictions look like? (visualization, endless types of front-end development) So yes, if you want to attack cancer through a data-driven process, there are TONS of ways for any kind of software engineer to join a team that drives that forward. (Disclaimer, I’m the founder/CTO of a YC-backed startup developing therapeutics in-house. We’re hiring people for all of the above roles to work on curing cancer. Check us out at https://reverielabs.com/careers https://reverielabs.com/careers)

How can a software developer contribute to cancer reasearch/treatment? Is there any hard problems? or manual work that could be automated?

by z3t4 7y ago

How can a software developer contribute to cancer reasearch/treatment? Is there any hard problems? or manual work that could be automated?

thanatosmin 7y ago

There are many hard problems and some that can be addressed by algorithms/automation. I think the best advice I can give is reaching out to a lab in your area that does cancer research. Most are happy to talk about what hurdles exist. We, for example, don't have the one true solution to cancer, but a whole lot of computational and algorithm needs that will improve our understanding of the disease.

jaimex2 7y ago

Well, they are tackling the problem medically. Why don't we try and engineer around the problem. All cancers exist for the same reason - our immune system isn't picking them up. Ideas? 1. Nano bots to replace immune system 2. Blood monitoring kits like Theranos tried. 3. Inmune system training kit that tries to encourage attacking cancer cells ( huge backfire potential ) (Disclaimer - I have no idea what I'm talking about )

abhikshah 7y ago
Your intuition here is great. 1. Nano bots -- no idea; outside my wheelhouse. 2. Liquid Biopsy -- many companies are working on diagnostic tests to detect cancer early, monitor treatment, detect recurrence, etc. Some of these products are already available but most are in R&D phase. 3. Immuno-Oncology -- the most promising development in cancer treatment in a long time. Successful tumors evade the immune system by essentially hiding themselves. Many companies are working on treatments to assist immune system in different ways. Some products have been in the market for a while now and have been pretty successful.
- rayhendricks 7y ago
  There is tremendous potential in Immuno-Oncology. I worked with umbilical cord blood [hematopoietic stem cell] transplants and this area really has tremendous potential for tech that only started being used in the late 80s to 90s. IMO much of the immediate potential for progress in software development will be with the legal and ux itself of ten tech though. Apart from a few companies the software is old, buggy, and has not or will be very slowly updated. One idea that comes to mind is making vastly improved LIMS and electronic patient recodkeeping software, as what is presently being used [bbcs] is from the 80s although this could be accomplished with just a front end written for it.

tejtm 7y ago

Work for Universities (for P.I.s housed at universities) for less than you are worth on the open market. (And still be resented by profs making less) Soylent data (it is made of people), is hard because it has all these lawyers attached to it. Figure out a trivial/foolproof way for EHRs to be satisfactorily anonymous for the legal departments to allow sharing but still be useful. (I won't be holding my breath) A concrete thing without any "hard" bits There is an open source tool named Protege that is ... err... the best tool of its class ... fix it or make a replacement []https://protege.stanford.edu/ https://protege.stanford.edu/

optymizer 7y ago
I worked for 5+ years for a PI at a prestigious institution. Overall my experience there was great. It was a lot of fun too. I got to design and implement fairly large projects early on as a junior engineer. I could use any tech that I wanted. I had maybe two dozen users at best, but I interacted with them weekly if not daily. That said, I was barely making 50k. Now I'm a senior engineer at a FAANG and though I am more financially stable, I am not having as much fun. I routinely push code to millions of users now, but I don't see any of them. I suppose the FAANG is a different kind of fun, but sometimes I just miss being the guy who's coding this awesome tool that's going to further scientific research, and your post reminded me of that. Maybe when I retire I'll go back to help some PIs with their software issues. I know they need the help.
- iandanforth 7y ago
  To put you on the spot. It would be great if "maybe when I retire ..." was an actual plan you had. It sounds like you have the opportunity and ability to personally make a difference, I sincerely hope you do. :)
  - optymizer 7y ago
    Thanks for the vote of confidence. I think it's early to make concrete plans though. I have a few other ideas to try out before I turn to academic research.

gww 7y ago

There is a lot of data being produced in these studies and outside of them. There are so many areas that a software developer could really benefit these projects. For example, a lot of bioinformatic software that is released is designed poorly, non-functional or hard to adopt. I wish there was a better way to integrate bioinformatics research with better software development principles. Unfortunately, there isn't a lot of motivation to make good software as the end-goal in most cases is to just get a publication and move on. There are examples of groups that really do put a lot of effort into quality software such as Seurat [1] or scanpy. Another area is trying to manage and process the datasets in large studies -- especially meta studies. Even for some of my small projects I dedicate a huge amount of time trying to curate random tables from publications, convert gene identifiers etc. [1] https://satijalab.org/seurat/ https://satijalab.org/seurat/ [2] https://icb-scanpy.readthedocs-hosted.com/en/stable/ https://icb-scanpy.readthedocs-hosted.com/en/stable/

Aperocky 7y ago

I would think there’s a lot, especially with molecular biology taking a computational twist.

chriskanan 7y ago

I work at a start-up (Paige) working on creating an AI-powered software platform for improving cancer diagnosis and treatment. We have a bunch of job openings (both AI and non-AI) and have raised over $70M. There are a handful of other companies out there working in this space, but there is a ton of opportunity for software developers to contribute. Feel free to email me (see profile) if you would like to talk about it.

whoisterencelee 7y ago

Take a look at boinc there are many cancer related computation projects

asdff 7y ago

Read up on the state of the bioinformatics field and get a feel for the tooling used in typical pipelines. There will be a lot of R and high performance computing. There's no shortage of work to be done.

TristanDaCunha 7y ago

If you make a lot of money, almost certainly the best thing you can do is earning to give¹. Your impact would be far greater again if you were to donate towards any cause other than one which mostly victimises wealthy people.² Instead of cancer victims, you could help poverty victims or animals in factory farms. ¹https://80000hours.org/articles/earning-to-give/#should-you-earn-to-give https://80000hours.org/articles/earning-to-give/#should-you-... ²https://www.effectivealtruism.org/articles/introduction-to-effective-altruism/ https://www.effectivealtruism.org/articles/introduction-to-e...

rmtech 7y ago
That's not an answer to the question that was asked. Some people might not want to help animals or people in the third world, they might specifically want to help cancer patients. Furthermore if someone is looking for the most important thing to work on, it almost certainly isn't animals or third world poverty, though it also probably isn't cancer either (unless they have an unusually efficient way to help), because cancer is basically the least neglected cause in the world, as well as being highly intractable. If you want something a lot more impactful than working on either of these things you have to think outside the box, do something that few others are working on and that could have a large impact in a way that is not well-known.
- gus_massa 7y ago
  > as well as being highly intractable. It varies a lot with the type of cancer, how fast it grows, how advanced it is, and a thousand of additional factors. https://en.wikipedia.org/wiki/Cancer_survival_rates https://en.wikipedia.org/wiki/Cancer_survival_rates Cancer is not a single illness, but a family of related illnesses, the main problem is that we don't have a different street name for each one. Imagine viral infections. What is the survival rate for viral infections? It can be a common cold, or Ebola, or somethin in between.
  - rmtech 7y ago
    Cancer is a group of illnesses that share a key common trait of uncontrollably dividing cells. But when I say intractable I mean that the amount of output in lives you get per dollar of input is small compared to other issues that you can help with.

DrScientist 7y ago

Lot's of ways - just look at the job pages of Cancer institutes/hospitals, Universities and research institutes or biotech/pharma companies. There is a huge amount of scientific and clinical data to make sense of - a lot of it in the public domain. Understanding the mutations at the molecular level is only a start - if you want to treat then you will likely need to understand how that mutation manifests into biology - what processes are affected and there you get into the very complex networks that is biology. But if you don't have a science background, it doesn't matter as most of the actual work is data management, processing and wrangling, before you can get to the insight bit. A lot of the data is being generated a huge scale as well - so making some of the existing analysis fast is also needed. A lot of the scientific software in the bioinformatics area can be found on github - so there it's as accessible to collaboration as any other github project.

probably_wrong 7y ago
> Lot's of ways - just look at the job pages of Cancer institutes/hospitals, Universities and research institutes or biotech/pharma companies. I'd be slightly weary of putting "pharma companies" in the same list, or at least not without the following warning: Pharma companies are still companies. That means: research will be often killed because it's not in the company's financial interest to pursue it further: if your drug is better but the market for it is small, your drug won't make it. It is not unheard for a company's plan for cancer to be "we'll wait until someone else does it and then we'll buy them". Pharma companies still fund their own research, and they are still putting out new, more effective drugs in the market. They probably pay better, too. But if you're making a career change because you're idealistic about "making the world a better place", a pharma company might not be the best move.
- natechols 7y ago
  > if your drug is better but the market for it is small, your drug won't make it As written, this is not what actually happens. The only way to know if a drug is "better" is to run expensive (and risky) clinical trials on it. Big Pharma wouldn't even bother going that far if the market isn't sufficient to make a profit - given the extremely high rate of failure in clinical trials, they never would have started the program in the first place. I realize this may seem like a minor semantic quibble but there is an awful lot of disinformation like "Big Pharma could cure cancer but it's not profitable" floating around.

ankitvgupta 7y ago

Cancer therapeutics development effectively boils down to a massive-scale optimization problem over a highly multi-dimensional surface. The status quo in the industry is to say "let's find a sufficiently good local optimum by having humans largely-manually try to make transformations to known molecules" in this space. But with software, we can address this issue way more systematically. Here are some questions we can ask (and answer with software) to drive this process more rationally: * How might you represent the molecules that define this space? (lots of graph theory, linear algebra, vector math) * How would you model their biochemical properties? (w00t supervised machine learning, but also physics simulations) * Once you build a model for a properties, how can you deploy that model at billion-scale to start searching this space? (containerization, distributed systems, k8s) * How do you iteratively improve your compounds (generative machine learning, evolutionary optimization, lots of search/RL methods) * Once you choose a compound you like and get some experimental data about it, how does that new ground truth value change your model? (data warehousing, data pipelining) * If that data is valuable, how do you keep it safe? (network security, ACLs, virtual private cloud configurations, VPNs, etc.) * How can we visualize what our data and predictions look like? (visualization, endless types of front-end development) So yes, if you want to attack cancer through a data-driven process, there are TONS of ways for any kind of software engineer to join a team that drives that forward. (Disclaimer, I’m the founder/CTO of a YC-backed startup developing therapeutics in-house. We’re hiring people for all of the above roles to work on curing cancer. Check us out at https://reverielabs.com/careers https://reverielabs.com/careers)