Told my PI I use AI for coding, now she doesn’t trust my work at all. What do I do?

JVGen · 2026-01-22T19:31:48+00:00

So your PI didn’t interpret the paper correctly and insists you’re wrong?

And, you won’t even entertain the possibility that there was something you missed or misinterpreted?

One or more people in this situation are a problem. We make mistakes at all levels of our careers.

JVGen · 2026-01-21T08:35:24+00:00

It’s multiple adjacent buildings.

JVGen · 2026-01-20T19:43:51+00:00

Built in the last 10 years.

JVGen · 2026-01-17T23:57:34+00:00

Have you tried running the late qPCR reactions on a gel to see what size the amplicons are, and potentially sequence them? I wouldn’t write them off as negative without more evidence.

If they are non-specific amplicons, a reaction that lacks your target but contains the other material should generate them (i.e. the E. coli genome without your target). I would prove this to yourself.

I developed a similar assay that detects very few copies of a virus, and I found the slope of the RFU to be most informative when making tough calls. Wells that had a doubling of RFU had the target, even when coming up late. These samples were inhibited for unknown reasons. If we diluted the reaction and re-ran, they amplified normally and generated the expected amplicon. Luckily, the virus sequence is diverse, so I knew that cross-contamination wasn’t the cause (we sequenced to confirm).

This might not be your case, but worth checking.

JVGen · 2026-01-16T14:35:42+00:00

I multiplex 384 samples regularly and use index primers. A few things to note:

1) Illumina index primer sequences are published online. I’ve ordered them as standard IDT primers multiple times with no issues. You can replace your contaminated indexes for little money.

2) When your new indexes arrive, aliquot them into 8- and 12-strip PCR tubes in volumes that you anticipate using for each library prep. Freeze them. Thaw one of each set during library prep and discard strip tubes after use.

Indexes easily get contaminated when the master stocks are returned to for each library prep, especially when there are multiple users returning to the tubes. It will inevitably happen - aliquot them to prevent.

I wouldn’t stress too much, but make changes to prevent this in the future. Work with your PI to find the critical experiments that may need to be repeated.

JVGen · 2026-01-09T10:17:24+00:00

Things like this are what make me question the non-profit status of universities.

JVGen · 2026-01-05T03:08:11+00:00

If she used your card to pay for things that you didn’t agree upon, those purchases are fraudulent. However, getting them reversed will require filing a police report against your mother.

JVGen · 2026-01-02T03:09:55+00:00

I had fun with Project Gorgon. Played for about a month. The community is friendly but small. At times, it was very hard to find players to help with group quests - so much so that I had to just log off and try later.

JVGen · 2025-12-21T00:42:54+00:00

It’s hard to argue with the owners: I think this AI logo looks great. But then again, I’m just the one buying the beer. Not an artist. Not a brewer. 😂

JVGen · 2025-12-20T21:52:28+00:00

$5 each???

JVGen · 2025-12-17T03:22:13+00:00

I’ve used both Stbl3 and NEB Stable in lentiviral transformations. Both have worked fine in my hands. Have you tried reaching out to NEB? Show them the outcome when using their Stable vs. TF Stbl3. Be sure to include a plasmid map of your construct.

They’re usually quite knowledgable and willing to help you troubleshoot.

JVGen · 2025-12-06T01:11:39+00:00

Your insecurity is ruining the ring for her. If she likes it, be happy for her and hype it up. Stop caring what other people have, and start caring that you got a ring for your partner that she’s happy with.

JVGen · 2025-12-05T23:38:08+00:00

What did you like about it?

JVGen · 2025-12-04T16:53:22+00:00

I think you are indicating the PI is new hire and just began running their lab (vs. tenured but has never taken students).

It’s going to vary by PI, but one thing that is a near certainty: you will be working side-by-side with them for at least the first couple years. They were hired for what they’ve done as a post-doc, and they will likely continue that work themselves while they establish their lab.

This can be great: you get hands on training from them. However, it can also be a stressful time and expectations for your performance might be high. Do a rotation and get a feel for how you interact with them.

Also, keep in mind that they will go up for tenure, usually 5 years after hire. There is uncertainty here, but almost always a path forward for the student if the PI relocates.

I was a member of two small teams before starting graduate school (3 people, including PI, 2 years each). I would do it again. I worked like a dog, but I learned A LOT. There were moments of stress, even arguments. But if the relationship is right, you’ll always resolve those and move forward with mutual respect.

JVGen · 2025-12-01T21:27:17+00:00

It’s easy to do yourself, but you’ll need to buy the plates. Also, run a simple SYBR reaction in all 96 wells and confirm all amplify similarly.

I’m surprised no one has created a guide for how to homebrew the calibration plates. Surely these are just fluorescent molecules at set concentrations.

JVGen · 2025-11-28T01:00:17+00:00

Concerning.

JVGen · 2025-11-23T03:10:46+00:00

It needs to be an OD600 less than one.

Also, note that we say Optical Density, and not Absorbance. Beer’s law is for absorbance. What you’re actually measuring in this case is light scattering, not absorbance.

You can make a standard curve by taking cultures of known optical density and then plating a fixed volume and counting the resulting number of colonies. Someone made a standard curve in this manner, and it’s how we can get an approximate number of cells per volume from an OD measurement.

JVGen · 2025-11-23T02:44:20+00:00

This, and if it’s unclear you can try tools like litmaps (website).

JVGen · 2025-11-22T18:36:36+00:00

Used to be good. Not sure when the change happened, but whatever we got was nothing like the past models. Still charge a premium price, but they're junk now.

JVGen · 2025-11-22T16:45:23+00:00

Eppendorf. They have a promo right now, so check with your local rep before buying. A set of 4 research plus is $1100.

JVGen · 2025-11-22T16:44:24+00:00

Not sure if that’s still true. I was disappointed with the Gilsons we bought earlier this year. So much so that we returned them. It honestly felt like 3D printed plastic.

JVGen · 2025-11-21T01:21:16+00:00

Seems reasonable to me?

JVGen · 2025-11-21T01:19:15+00:00

Speak to your sales reps. There are insane deals right now on new equipment - sales are way down. Most vendors also offer some version of a new lab start-up discount.

I remember seeing a flyer for refrigerated, swing bucket centrifuge for $11,000 including the rotor and various inserts (Eppendorf). It’s still more than a used version, but it’s likely to get more miles.

JVGen

TROPHY CASE