Adam Retchless, Ph. D.

Tim Chambers established a list of journalists on Mastodon. It currently has 1400 names on it, added between 11/4/2022 and 12/27/2023. Many of these accounts are dormant, so I filtered them down using standard Mastodon tools — I loaded the list, removed ‘dormant’ accounts (no posts in the past month), and was left with 303 active journalists on Mastodon. I then exported that list in case anyone wants to play with it:

This could probably be done more elegantly with the API, but I have not worked with it. The original list is below.

If you care about Atlanta (The ATL) and want to participate in the Fediverse using Mastodon, sign up at theatl.social. ‘TheATL.social’ is an LLC run by volunteers (including myself) who want to improve the ability of Atlanta residents to connect and talk about their city. In addition to the primary Mastodon instance, theATL.social runs a Lemmy instance called “Y’all” for more in-depth discussions of topics and the news.

I’ve confirmed that I can send comments from my Mastodon account to this blog by responding to the blog post. That’s cool. The comments still go into the same moderation system.

The main limitation is that only public comments show up from the WordPress side. That makes sense, because WordPress doesn’t have a way to receive private messages. However, no feedback is given to the sender… so they send you any non-public message and it will just disappear into the void (unlisted, followers only, tagged only)

Also, I tried tagging my Mastodon account from here, and it did not work.

I’ve been participating in the fediverse for about the past year with the Mastodon community at mstdn.science. Microblogging has it’s benefits, but it’s not really my favorite way to write out my thoughts… the full blog is really more my style. So I think I’m going to write out at least a few posts here to organize my thoughts regarding the fediverse. Conveniently, WordPress recently released their v1 ActivityPub plugin, so I’ve activated that and confirmed that I can follow this blog from my mstdn.science account. It’s a start!

In describing a new HIV evolution paper in Science, Dan Graur (aka “Judge Starling”) writes:

“The only thing “novel” about the analysis was the use of a Bayesian method for phylogeographic inference. Interestingly, as in all examples of its use that I have seen so far, the method tells you nothing you do not know or cannot infer by much simpler means.”

I haven’t looked at the paper in question, but I have noticed this common infatuation with pointlessly (even recklessly) complex statistical methods.

As if there weren’t enough reasons to abandon the penny in the USA, I just learned of a new reason to ban the penny from my home — they are poisonous. The problem is that when pennies are swallowed (by an infant, for instance), the zinc innards can be dissolved by the stomach acid. This can lead to two medical issues: the dissolved zinc can create an ulcer, and the copper shell can cut through internal organs. This issue was brought to my attention  by the first-hand story of a health-care provider whose patient died from internal lacerations caused by a penny. I cannot find anything online about incidents like this, so it is apparently extremely rare. The problem of zinc poisoning is better documented. There’s a chance that my source was confused about the mechanism by which the  penny killed the child, but given his proximity to the case and the details he provided, I’m pretty confident that he knew what he was talking about.

The risks may be pretty low, but given that pennies are nothing more than clutter in my house anyway*, I’ve decided to ban them from my house. I’ve been leaving them behind in stores, but I should just start telling cashiers to keep them (consider it a tip, if you’d like). One of the local stores has a policy of rounding to the nearest nickel, which I wish more stores would adopt. Frankly, I’d be happy if they rounded to the nearest dime or quarter.

Having completed my rant, let’s see a  demonstration of the chemical reaction — you can dissolve the zinc core of a penny at home if you’d like:

I did this using salt and vinegar, as suggested here.
Another neat trick to plate the penny with zinc, and then turn that plating into brass:

p.s. My web-search for pro/con penny arguments came across an essay at Forbes called Don’t You Dare Eliminate the Penny, as one of the first hits. The argument is so ridiculous that it actually strengthened my confidence that the penny should be eliminated, on the grounds that penny advocates have absolutely no basis for their position. However, I was able to find some better arguments by going to Wikipedia, though even some of these were very weak. As is usual with debates, Wikipedia has a decent distillation of the major arguments.

*pennies are worth 5 seconds of minimum-wage work. It’s hardly worth taking the time to pick one up from the floor if you have a full time job.

**p.p.s. This post gave me a few good ideas for educational science projects…once my kids are old enough to not put the pennies in their mouths. So maybe pennies have value after all!

Previously, I griped about the business practices of Research Gate and swore that I would not participate in their community.

Like many online communities, RG sends out plenty of spam, but this is particularly annoying spam — the “from” lines shows the names of colleagues on Research Gate who have attempted to create links to me on RG. In contrast, LinkedIn clearly identifies itself when sending updates and connection requests. Since I have a LinkedIn account (which controls the frequency of these emails), those emails aren’t even spam.

So, if you participate in Research Gate, that company will use your name to spam your colleagues. Classy.

There are many reasons to use Linux, but the main drawback is a lack of support for third-party software. When I set up my new Fedora Desktop, I was caught off guard by the fact that Box.com does not provide sync software (there is a hack, but it’s not really a solution) — I hadn’t realized how dependent I had become on Box.com to backup my work and synchronize my computers. UC Berkeley contracts with both Box.com and Google to provide cloud storage, but neither of them come through in this situation.

However, by free Dropbox account has come to the rescue! The Dropbox client had one minor glitch, and otherwise works perfectly. Now I’m shifting to using them for my day-to-day backup, and limiting my use of Box and Drive to sharing large files.

Thanks Dropbox!

Here is some “advice” on how NOT to be a bioinformatician (i.e. how to make bad software for biology). This makes me ask the question: “Why be a bioinformatician?”

Much of the advice in here makes me think that a lot of “bioinformaticists” don’t really have a good reason for doing what they do. I have to say that I’ve seen a lot of bad biology-focused software. I’ve even heard respected biologists declare that the entire field of bioinformatics is worthless (at least, the stuff published in bioinformatic-focused journals is worthless).

So what is a bioinformaticist trying to achieve?

One approach to bioinformatics is to create software that addresses one’s own research interest. The funny thing is, these typically are not the programs that are published in bioinformatics journals — they are published in biology journals. When I look at the software tools that have been most useful to me, they are not made by people I consider bioinformaticists — they are made by biologists, who are programming computers as a tool to solve problems that they are interested in. Even when these scientists are trained in statistics and CS, they are still tightly connected to a particular biological community and they are designing software that answers research questions that this community cares about. This often allows them to answer questions that nobody has been able to answer before.

The other approach to bioinformatics is to build a tool that others will use. This seems to be the focus of the linked SCFBM article.

All too often, these software/algorithm development projects aim only to produce incremental improvements in existing methods (e.g. making them more accurate or faster or user-friendly). These typically don’t lead anywhere, and I don’t consider these to be appropriate academic projects — this type of optimization should be performed within teams that are interested in some sort of mass-production and have real accountability for the performance of their software (e.g. at commercial firms). Publishing this type of work is an invitation for BS.

There is still space for applying serious CS to improving bioinformatic tools, but these should focus on radically different approaches to the analysis, so that they enable order-of-magnitude improvements in the efficiency of the algorithm.

This same problem of misguided motivation is seen in the plethora of web services that have emerged during the mass-sequencing era. I have been very frustrated by these, since the vast majority of them simply waste my time by promising things that they cannot deliver. Many of them are not maintained — which makes perfect sense given their limited utility to begin with.

If you are going to make a software tool “for biologists”, you need to ask yourself whether it will be useful enough to be worth making properly and maintaining it. If your service is very narrowly focused, are you going to bother maintaining it just to serve the one user per month? Are biologists going to bother discovering your service if it nearly duplicates an existing service that they are already familiar with (e.g. NCBI)? Will they ever hear about it if it provides a single narrowly focused service? Does the service actually provide useful information, or does it simply make predictions that a biologist will need to test anyway if the prediction really matters?

So before trying to figure out how to properly develop bioinformatics software, figure out why you want to make these tools at all.

A student brought my attention to Repast when he did some modelling with me this past summer. This is an agent-based modelling (ABM) platform, primarily for Java (though there are also tools for other languages). It is apparently based on an earlier system called “Swarm”, which I’ve heard is slightly more powerful and slightly more difficult to use. Since I was already familiar with Java and Eclipse (of which Repast Simphony is a derivative), we decided to give Repast a shot. In addition to the core agent-manipulation libraries, Repast has powerful visualization tools, active developers, and a decent-sized user community.

The main difficulty in using Repast in the dearth of documentation. This post is meant to help on that front by collecting links to the materials that I have found useful (as much for my own use as anyone else’s). But before getting into that, I’ll provide a little context for why Repast is interesting and perhaps why its documentation is so difficult. Everything I write is based on Repast Simphony 2.1, which is built on top of Eclipse Kepler (Build id: 20130614-0229).

One appealing feature of Repast is that it provides interfaces that can hide the inner-workings from the user, allowing researchers with different levels of programming skills to access the tools. At the simplest end in ReLogo, which is similar to the very accessible NetLogo (apparently both derived from something called Logo). I played with this briefly, but got stumped on how to do simple arithmetic in this language. Rather than learn another language, I  transferred over to the Java side of Repast, which promised greater power anyway. Even here, the core of the modelling engine is still hidden from me, which has become an issue when I wanted to access the scheduling mechanism. It seems that one consequence of developing these different levels of accessibility is that the user community is split into three groups, each of which requires separate documentation.

Since I want to learn about the advanced features of Repast, the obvious place to go is to the developers, who are active on the Repast-interest mailing list. However, I don’t want to bother them with questions that they’ve answered a million times, so I should first search the list archives (as suggested on the sign-up page). But the archive page does not include a search feature (really?). So I do a Google search, and find that someone else asked for a solution on the mailing list, and was told to try searching on Nabble. This is way too meta (To reiterate, I did a Google search to ask how to search the Repast-interest archives, which directed me to a Nabble page contaning an old discussion from Repast-interest, where the answer was that we should use Nabble.)

Another good resource is the large collection of demonstration models. The downside is that there is no quick way to find the model that demonstrates the technique that you are interested in. In my experience, the StupidModel series of models shows the most sophisticated methods.

The Repast GUI provides a powerful interface to the models, but make it difficult to just open up the source code and track the logic. For instance, the main class for all GUI models is “RepastMain”, which is a quite terse and cryptic launcher. As I understand things, Repast launches the GUI (which appears to be encoded at a lower level than Java), which then gets its instructions from a collection of XML files that are associated with your project. For Batch files, the main class is called BatchMain (but the header indicates that this is deprecated in favor of RepastBatchMain).

After poking around the web a bit, it seems that the classes to use to get at the core of the model are RepastEssentials and RunEnvironment.

With all that searching for answers, I wonder does StackOverflow have information about Repast? They don’t seem to have anything specific to Repast, but the do have some discussions of Agent Based Modelling where they discuss Repast in the general context of ABM.

Other links I found helpful/interesting:

Stackoverflow discussion of ABM approaches…and another.

Wikipedia comparison of ABM tools

Repast self-study guide (links to tons of resources)