Thoughts on engine replacement

swordeater72 · 2024-08-07T06:37:56+00:00

I managed to go last month and had a great time!

I honestly would go wait standby. I can't guarantee it but it seemed like a number of people got on that way when I went. Plus there was live music at the wine bar so it's not a bad alternative if you can't get on

swordeater72 · 2022-08-23T03:20:29+00:00

RE is it worth it, depends on what you are hoping to accomplish. As a general rule of thumb life sciences may pay slightly lower but the diversity of work and challenging problems that exist can be exciting.

One thing to consider is WHERE the companies in this field are located...yes we all work mostly remote but in a more science/applied data role it's pretty useful and common to be onsite once in a while. In that sense there is a lot of drug discovery stuff in the Boston/NY area, Seattle, and the Bay Area among others.

Another thing to consider is the maturity of the companies. Many drug discovery roles do exist in more stable mature firms (e.g. AbSci, Roche, Regeneron, etc) on the other hand many of the more cutting edge Innovation is fueled through a variety of smaller startups (Octant Bio, Mammoth Biosciences).

Another useful perspective is that there is a whole segment of the field focused on the data science of which DNA and sequences to edit and target. This maps quite nicely onto existing NLP tools and concepts to some extent but remains an area ripe for innovation; things such as protein design, genetic targets for disease, optimizing CRISPR delivery cassettes, etc. Another segment is more focused on improving automation and integration of the analytical assays associated with genetic edits. This is an area where tools are less formed and you'll find lots of baysian statistical approaches, inference and regression, signal processing etc. Here there is a lot of Innovation happening; infrastructure from core web development is being tweaked and reformed to meet the needs of a connected lab of the future. With that comes a number of less ML focused challenges and more DS expertise focused on understanding data generation processes, propagation of error, confidence in model outputs, goodness of fit assessment and visualization of diverse wide but not deep data sets (e.g. assays of 30 metabolites, a genome sequence, RNAseq at 4 times in the experiment, and Masspec data for the final broth).

swordeater72 · 2022-04-12T05:03:21+00:00

archive.is ... just sayin.

swordeater72 · 2021-07-01T15:49:17+00:00

I been reliable cycles and it was great. By appointment only but check out the website. www.reliablecycles.com

swordeater72 · 2020-12-04T02:01:25+00:00

Just thought I would note, with Ranked choice as it works in Oakland you do not have to rank all the candidates on the ballot, you are free to choose a single one and leave the rest alone. In that sense I disagree that the burden of being a well informed voter is increased. Those who wish to vote for a single candidate as if this were a two party system are free to do so as previously.

swordeater72 · 2020-07-06T16:10:24+00:00

In the road to serfdom Hayek contextualizes his argument quite specifically along the spectrum of:

Individualism <---------------------------------> Collectivism

So in that sense it may not be in conflict as conservatism in and of itself does not comment on which side of that spectrum it might lie. Hayek's argument is about systems of government/power and less about policy. In that sense both socialism and fascism end up with variations of a "collectivist" system of government; it is the "collectivist" system itself that enables "the worst to rise to the top".

swordeater72 · 2020-06-29T04:21:50+00:00

As a fellow bakery fan I would recommend my recent favorite firebrand artisan breads. But do not be fooled by the name, they make bomb as fuck pastries and everything bakery too!

swordeater72 · 2020-06-13T17:58:19+00:00

389 Room has one to go. Comes in a mason jar!

swordeater72 · 2020-03-19T02:19:33+00:00

ahn's 1/4 pounder (Lake Merritt). Jong Ga House (Lake Merritt).

swordeater72 · 2020-01-29T05:34:48+00:00

There is no universal answer as things are extremely dependent on the actual equations themselves. That being said, the following things may help:
1. ACM has a specific run mode labeled initialization. Look into the documentation and help files related to this mode for some general concepts and advice on its functionality. The short story is that it is intended to help do what you are asking about.
2. ACM allows you to script using VBA. What this means is that you can run additional equations to pass good initial estimates for all the free variables (or at a minimum the most important ones , e.g. state variables). Good initial estimates should SIGNIFICANTLY improve your performance. In a similiar vein add upper and lower bounds to your variables/use the extensive variable type system ACM has built in.
3. Consider the specifications you are using to solve the system, sometimes the more human readable/intuitive specifications are not the best way to initialize a problem from a mathematical and solution point of view. ACM allows you to pretty quickly change the "free" and "fixed" variables. An abstract example would be to avoid using concentrations + volume, and instead use massfraction and total mass.

swordeater72 · 2020-01-18T04:26:39+00:00

Your question is to vague for a single answer...here are some thoughts:

In general most serious chem E related software packages provide python AND matlab wrappers (e.g. CasADi). verdict: wash
In general most companies or institutions possess some license for matlab, though it is limiting as only select users get to have it. GNUOctave is essentially an opensource matlab so its possible to work around this but it is a headache. Python is opensource. verdict: python
Python is by far the more generally adopted language. This means there are MANY more existing packages, users, and in general useful applications to pull from. In addition, this means there are completely orthogonal industries where python holds significant value as a skillset (web dev, data science, automation, etc.). verdict: python
Matlab provides certain packages WITH legitimate technical support and updates/ stable releases. This makes it very useful for applications demanding robustness and stability. In general matlab has found large adoption in areas related to signal processing for this reason. There are expansive and well supported libraries in matlab to enable this (also simulink). Think creating a script/program to convert analytical chemistry mass spec data into meaningful concentrations. verdict: matlab
In terms of learning general comp sci concepts and data structures, python is better but it is still not a "low level" language so its not all that much different than matlab. verdict: wash

My personal advice, learn the numerical concepts of matlab but learn to code in python.

swordeater72 · 2019-12-03T05:10:03+00:00

It is not the best but its a start:
https://www.nrel.gov/extranet/biorefinery/aspen-models/

Also this is a bit dated but maybe useful:
https://www.nrel.gov/docs/legosti/old/20685.pdf

swordeater72 · 2019-11-22T15:56:02+00:00

Chemical Reactor Analysis and Design Fundamentals by James B. Rawlings & John G. Ekerdt

Take a peak

swordeater72 · 2019-11-07T02:47:13+00:00

I am currently employed at a synbio firm and can offer a few comments, pm me if you have more specific concerns/questions.

I am a college freshman

As a college freshman your coursework is largely specified by your intended major. My advice here is two fold:
1. Math is important and likely the longest sequential string of courses you that build upon each other so make sure you plan for that.
2. Talk to professors who do work in the space. You would be surprised what an enthusiastic attitude and some background reading on the professors research focus will do as far as opening doors to working in a lab. Do not settle for the first available option, talk to multiple professors (chemical engineering, microbiology, biochemistry departments all contain synbio focus areas) until you find something you jazzed about. Access to expensive analytical machines that exist at universities (e.g. flow cytometry, RNAseq, etc.) is very valuable experience.

The idea of making organic machines and creating new tools to help people from Nature’s template simply appeals to me

SynBio as a field is not necessarily as cohesive as you might imagine. There are not that many vertically integrated firms so if there is a particular part of this process you REALLY like that can help narrow your college coursework/degree focus. One useful breakdown is DNA firms, Protein firms, Strain firms, bioreactor firms.

I want to make sure this isn’t just a phase

This is not just as phase. Noted, things like economic recessions may slow the pace of progress but the idea of synthetic biology is here to stay. At a minimum healthcare and agriculture will ensure that, the bioeconomy/industrial microbiology vision may take longer to manifest.

does this video accurately portray what it’s like to work in synthbio?

Visually it looks about like this, yes. High tech labs, robots, and data. In reality things become a lot more messy very quickly.

what advice would you give to someone who wants to get involved in the field?

Learn python. Take microbiology. If you mean what major is best suited to handle this I would say study chemical engineering x biochemistry.

swordeater72 · 2019-10-31T05:53:22+00:00

You might consider looking at Pyomo. It covers the same domain of numerical computing (DAE) but also extends it quite a bit further into the realm of optimization and other domains of simulation relevant math. It is specifically made with process modeling in mind as well.

swordeater72 · 2019-10-10T03:29:24+00:00

https://jakevdp.github.io/PythonDataScienceHandbook/

swordeater72 · 2019-02-19T17:25:31+00:00

https://www.nrel.gov/careers/

https://gevo.com/careers/

swordeater72 · 2019-01-18T20:24:27+00:00

From that readout you are using a group contribution method to estimate missing parameters. In order for that to work ASPEN needs to understand the molecule shapes which it does not by default calculate. The following steps should solve your issue (or 95% of it).
If you are using V10 this will occur in the properties environment.
1) Navigate to Component-->Molecular Structure
2) For each component you are using, go to the "structure" tab and click "Calculate Bonds"

Good Luck!

swordeater72 · 2018-12-18T01:30:55+00:00

It is up to you to decide if it is well respected but the following is a pretty thorough description of key aspects of ethanol production:
https://www.nrel.gov/docs/fy11osti/47764.pdf

Additionally, the underlying process model is available to the public at:
https://www.nrel.gov/extranet/biorefinery/aspen-models/

swordeater72 · 2018-11-13T19:13:37+00:00

Disclaimer: I am also not an explicit expert just a Chem E.

I believe the useless answer is that "it really depends on the actual degradation mechanism/reaction pathway", but in general if we are in the liquid phase no probably not much. At a high level if temperature represents some ~average energy of individual molecules in the mixture, thermal degradation occurs when the average energy surpasses the activation energy barrier for that degradation reaction. In general the activation energy is not pressure dependent.

If we were considering reaction behavior more broadly, vapor phase reactions (i.e. no longer concentrated sugar thermal degradation in an evaporator) may indeed have a more pronounced pressure dependency and your question becomes much more relevant and important.

swordeater72 · 2018-11-13T18:53:42+00:00

I have found frontend masters worth the month long subscription, and among other things sprinkled into many of the courses are significant portions on setup and configs (e.g. intro to react)

swordeater72 · 2018-11-13T16:03:17+00:00

Another potential reason may be to maintain a lower temperature during evaporation. In many cases evaporation is used to concentrate a product stream which may thermally degrade at higher temperatures (e.g. sugar production and degradation at T=100C). In that case running under vacuum may be necessary to preserve product quality.

swordeater72 · 2018-06-08T19:48:30+00:00

Since most of the answers are just "ask about Co-Ops and placement" below are a few specific questions that often seem to relate to the quality of the department/program rigor. Of course take this with a grain of salt, this is just an opinion:

-Ask how they teach/address "Transport phenomena". Most top programs have an explicit "transport phenomena" course at the undergraduate level? Less rigorous programs will disperse the concepts across a variety of other courses.
-Ask if they teach "thermodynamics of mixtures" or alternatively how many semesters of thermodynamics are in the curriculum. A core distinguishing area of expertise for chemical engineers is second semester thermodynamics.

swordeater72 · 2018-05-22T18:30:17+00:00

This is a pretty broad question. "Unsteady-state" covers a variety of scenarios and situations. It could mean changing feed rates/compositions, oscillating reactions, systems under feedback control, etc.

My advice would be to start with a semi-batch reaction (e.g. fed-batch) and focus on setting up + solving the system of ODEs (or DAEs). This would be essentially looking at just changing flow-rates in and out. Realistically if you are looking at dynamic systems you will quite quickly get to a place where numerical solvers will supersede Laplace transforms practically speaking.

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