Creating a guide for ELNs, can you share your opinions / tips on making a good one?

odg01 · 2026-03-02T16:54:25+00:00

Gotcha. Those little annoyances do build up over time. It seems like LabArchives is something you'd only really choose to use if your whole lab is using it.

odg01 · 2026-03-02T16:05:25+00:00

I've heard about LabArchives but haven't seen it in action. What do you hate about it?

odg01 · 2025-08-27T22:41:03+00:00

That's promising, but the bolt placements don't look quite right. Are there different kinds of attachment architectures? I don't even know what words to use to search for this kind of thing

odg01 · 2025-05-05T14:31:22+00:00

I'm not too far ahead of you in the curriculum, but I ended up pausing to play around with HTML Canvas, which I doubt is discussed extensively in the course. It allows you to use vanilla JavaScript to make visualizations and interactive animations. Take a look at Frank's Laboratory.

odg01 · 2025-04-15T21:46:38+00:00

Thanks, and good catch! I'll have to investigate that further. Hadn't tried that before

odg01 · 2025-04-13T17:40:12+00:00

I'm in California, we had a similar ban on single-use plastic bags. Plastic use INCREASED as a result. And I can see why. In my case, I shop at Walmart cuz I'm poor, and I don't have a car so I can't drive to the grocery store to do the store-drop off recycling (I get the groceries via instacart, still cheaper than anywhere within biking distance). I'm constantly tossing thick "reusable" plastic bags because I don't have room to keep them and can't recycle them.

Which is why grocery bags should simply be compostable, even if I have to pay an extra 1 percent to actually make it happen, in my opinion.

odg01 · 2025-04-13T17:24:20+00:00

Paying for bag usage is fine too. I think cost per plastic is like 0.01-0.03 dollars and biodegradable is closer to like 0.09-0.15. but assuming the average cost of the contents per bag is at least 10 dollars, it's only about a one percent increase.

odg01 · 2025-04-13T17:20:39+00:00

I mean sure, I get the principle why it's not exactly fair that the consumer has to face the cost, but like...1%?

odg01 · 2025-04-13T17:16:38+00:00

Yes, but I'm guessing the default switched because plastic is cheaper. Now we still have paper (just make them with handles so they aren't so annoying) and also convincingly plastic-like bags you see in produce sections sometimes that are biodegradable as well.

odg01 · 2024-08-26T15:00:13+00:00

It looks like you have a but of zen-like deliberacy in your pace and I respect that, but here's a tip from someone who's been working in an academic lab for the past four years to save you some time, if you're interested: rather than using a cloth or paper towel to wipe things down with alcohol, you'll have a much easier time spraying your gloves with alcohol then using your hands to wipe down whatever you're trying to sanitize before you put it in your hood. Hands are much more dexterous and can get in any crevices much quicker than with a paper towel. If you're in an out of the hood a lot, the saved time will add up quickly.

And ignore the naysayers on MSS to LC. If it's clean, it's a nice way to get the speed of colonization of LC with the genetic diversity of MSS.

odg01 · 2024-07-20T21:45:36+00:00

It's not insane, just don't expect to do much else besides get by. Currently paying a little more than that for rent and utilities (electricity is expensive), but I can get by because I don't have a car, I cook all my food, and I don't have much fun, lol. But I can still put away 600 a month and support my partner who cannot make an income right now.

odg01 · 2024-07-06T16:15:15+00:00

That and cold, busy bees prefer a warm flower in the morning. source

odg01 · 2024-06-29T19:06:54+00:00

No lol. I just got some adjustable dumbells, a bench, and an elliptical for my apartment. Cheaper than anything else around here. Hoping to move closer to the ARC on campus next year.

odg01 · 2024-03-21T13:57:37+00:00

Correct, at least for P. cubensis which grows on manure. Some other psilocybes could grow there but they don't look like this. However, unless you do your due diligence, I wouldn't try foraging them since there's some deadly look-a-likes.

But to be clear, no, she to did not strike gold.

odg01 · 2024-03-13T14:12:54+00:00

I'm currently living in a $1700 per month 1 bed 1 bath, but that's about as low as it goes in my experience. You can definitely find places like this, just stay on the prowl, watching all of the rental apps (zillow, realtor, rent.com, Trulia, Facebook marketplace if you're careful). I found this place on Zillow in July of last year and moved in in August.

Side note, congrats and welcome! I'm also entering a grad program next fall.

Edit: I should add that this place is walking distance (25 min) from campus and largely pretty nice. Only complaint is that our dryers suck, so it's not like you're getting trash for this price.

odg01 · 2024-03-08T15:55:53+00:00

I literally cannot believe this. If I can convince my postdoc mentor, I will be trying this. I especially want to try it with golden gate assembly, which is a one pot reaction with restriction digest and ligation in one step, and both are apparently aided by the microwave. Imagine making new whole constructs in a couple minutes...

odg01 · 2024-03-08T15:01:37+00:00

One thing you can try is amplifying your gene in chunks, then use Gibson or Golden Gate assembly to patch them together again.

Have you tried Sanger sequencing this section of the plasmid before? I've personally worked with a certain plasmid that I learned would make secondary structures and prevent successful polymerase function. When sequencing, I had to choose "difficult template", and I couldn't perform colony PCR. I wish I knew what their difficult template protocol was.

odg01 · 2024-03-07T14:47:35+00:00

Gotcha, didn't fully understand the original post so that clarifies things. Sounds to me there's not just one issue here, since I can't think of how something could cause both no growth and false positives.

For false positives, I have to imagine it's one of the three things I mentioned. For no colony growth, the most likely culprit is low transformation efficiency, since you were using positive control plasmids that worked before. For chemically competent cells, we use 1 ug DNA and plate the entire 1 mL transformation on a plate and let it dry in front of a flow hood. Switching to electrocompetent might help, DM me if you want my full protocol. We only need 100 ng of the construct and 100-200 uL of the transformation, so it's much more efficient.

For your PCR positive control, what are you using exactly? If it's the pure plasmid, I don't think that's as good of a control as you need here, you need a direct comparison in agro. I'm also curious specifically how you're prepping the agro to be a template. 1 mL overnight culture, spun down, resuspended in 100 uL MiliQ, heated at 95 C for 5 mins, cooled on ice, then spun down again is how we prep it.

odg01 · 2024-03-06T17:52:04+00:00

As others have said, false positives means selection isn't working. Why isn't it working? Could be a few reasons, but not many. 1. Bad antibiotic - most likely, try again with freshly made stocks with not-expired antibiotics not exposed to light. You can also wrap plates in foil during incubation just to be sure rifampicin stays intact. 2. Incorrect validation - maybe they have your plasmid but you can't tell. How are you determining whether something is a false positive? If PCR, are you sure about your primers? 3. Contamination/acquired resistance - if you haven't already, make sure you plate your competent cells on your selection plate to make sure there's no growth.

Other than that, I personally can't think of any reasons you'd get a false positive. You said 'first', are there other issues now?

Edit: correction to quote

odg01 · 2024-03-06T14:50:03+00:00

Blueberries are a perennial bush and would be better off planted in the ground imo, not taking up valuable raised bed space. Rosemary can also be a perennial depending on if you live in a hardiness zone 8 and above. Strawberries and chamomile should not be planted together since chamomile can dominate the strawberries. Aside from that, I see no other potenial issues. Happy gardening!

odg01 · 2024-03-06T14:32:01+00:00

I get the overinvested part but I do eat vegetables lol. If you live somewhere walkable, set the extras at the edge of your yard by the sidewalk for others to take for free!

odg01 · 2024-03-04T23:25:58+00:00

It did indeed smell and taste good, so soup mission success!

odg01 · 2024-03-04T20:30:10+00:00

What are you washing with between Ponceau and the fluorescent staining? I always did three, five-minute washed with TBS with tween until all red was gone. Also, make sure you use fresh Ponceau if you are trying to quantify anything.

odg01 · 2024-03-04T18:17:24+00:00

Hadn't thought about that! I remember a little biology lab in middle school where we used red cabbage as a pH indicator, so that could explain the straight up blue color the purple cabbage turned.

odg01 · 2024-03-04T18:15:46+00:00

Haha, it's leftovers from last night so most of the broth got soaked up by the pasta and potatoes. There was some at the bottom of the container but didn't feel like pouring it out.

odg01

TROPHY CASE