# New Plant Growth Chamber Subgroup **URL:** \ **Category:** Plant AWG Topics\ **Tags:** aiml, plant, plantawg, gl4hs\ **Created:** [February 26, 2026, 9:07pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926 "2026-02-26T21:07:41Z")\ **Posts on this page:** 20\ **Page:** 3
**Author:** ![amanda](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@amanda](https://awg.osdr.space/u/amanda)\ **Post date:** [July 12, 2026, 8:23pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/41 "2026-07-12T20:23:28Z")
Thanks for the concern! I was thinking that too, but I found a session that I think aligns well with our project (screenshot of it attached for anyone wondering!). However, if you (or anyone!) know of any conferences that are more aligned with space biology/life support, I’d be really interested in learning more; I know of AbSciCon, but that seems to be taking place next year/already happened this year. ![Screenshot 2026-07-12 132038](https://us1.discourse-cdn.com/flex001/uploads/osdr/original/2X/0/0b16c70da392f72bc4d4393927d5ac10b0d5a3a6.png) ---
**Author:** ![rtscott2001](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/rtscott2001/32/5_2.png) [@rtscott2001](https://awg.osdr.space/u/rtscott2001)\ **Post date:** [July 13, 2026, 2:15am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/42 "2026-07-13T02:15:58Z")
Oh wow, this is awesome to learn about! It’s great that AGU is more interested in human spaceflight and biology. Interesting, there was VERY little interest by AGU a few years ago when we attended. Thanks for sharing! Cheers 🚀 ---
**Author:** ![GasMan](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/gasman/32/2042_2.png) [@GasMan](https://awg.osdr.space/u/GasMan)\ **Post date:** [July 13, 2026, 5:00am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/43 "2026-07-13T05:00:10Z")
@dr.richard.barker [@PlantAWG](https://awg.osdr.space/groups/plantawg) NB06: [NB06: Light vs Dark - Gravity's Series v1 | Kaggle](https://www.kaggle.com/code/gastondana/nb06-light-vs-dark-gravity-s-series-v1) is officially live on the repository hub. I have expanded the pipeline into a multi-factor interaction series basic capstone to explicitly isolate the environmental delta you highlighted. Instead of simple pairwise comparisons, the engine now models the light × spaceflight interaction term natively using a 2x2 contrast design matrix in PyDESeq2. The code handles probabilistic RSEM expected count quantization, suppresses outlier variance across all 28,187 genes via Cook’s distance mitigation, and isolates high-confidence targets. ### Key Analytical Takeaways: - **The Interaction Cloud:** Out of the entire transcriptomic landscape, the pipeline isolated **35 specific genes** that demonstrate a significant hardware/gravity-specific interaction ($p\_{adj\_ISS} \< 0.05$, $|\text{Interaction LFC}| \> 1.5$). - **Phenotypic Variance:** The vast majority of the plant’s genome handles light treatments uniformly across environments (forming the baseline cloud). However, these 35 target outliers (such as top hits `AT1G21528` and `AT5G20150`) have their standard terrestrial operational logic completely overwritten when lighting stimuli intersect with microgravity. The final visual canvas has been built as an interactive 4-quadrant scatter plot inside an isolated HTML iframe backdrop to ensure seamless browser rendering. You can hover directly over individual coordinates to extract exact gene IDs and Delta-LFC values for downstream functional analysis. ### Next Phase: Hosting an Open Benchmark Suite (30+ Models) To scale the utility of this framework for the AWG, my next step is transitioning this 6-notebook pipeline into a **standardized evaluation benchmark** across **30+ state-of-the-art computational and foundational models**. To ensure this directly serves the group’s operational goals rather than being a purely academic exercise, the benchmark will evaluate the models on two core criteria: 1. **Data Engineering Resilience:** Testing how robustly these 30+ models can autonomously ingest raw, uncurated space-biology assets, self-diagnose technical pipeline artifacts (like the RSEM decimal parsing shifts and whitespace indexing anomalies we solved here), and execute clean alignment without manual human cleaning. 2. **Autonomous Signal Convergence:** Measuring their ability to independently navigate high-dimensional genomic noise ($p \gg n$) and accurately converge on the exact same high-confidence interaction networks and biological pathways isolated by our baseline framework. This transitions the “Gravity’s Series” from a static walkthrough into a functional validation suite. The goal is to establish a blueprint that helps the subgroup automate and standardize the processing of incoming spaceflight data packages as they hit the repository. The capstone notebook and the full workflow history are open for exploration on the [OSD-120 Code Hub](https://www.kaggle.com/datasets/gastondana/osd-120-cara-arabidopsis-iss-rna-seq-rrnarm/code). Feel free to fork, adjust the LFC thresholds, or build out the functional pathway tracking where the science needs it next. Thx! ---
**Author:** ![rtscott2001](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/rtscott2001/32/5_2.png) [@rtscott2001](https://awg.osdr.space/u/rtscott2001)\ **Post date:** [July 13, 2026, 3:32pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/44 "2026-07-13T15:32:50Z")
@amanda - can you share the link, or the screenshot with me for this whole session (P003) – trying to get a sense of who is organizing it, and whether we urge AWGers to participate. Also I can only find AGU2025 with poster titles on this, so double checking this is for AGU2026 Thanks! ---
**Author:** ![amanda](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@amanda](https://awg.osdr.space/u/amanda)\ **Post date:** [July 13, 2026, 3:59pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/45 "2026-07-13T15:59:09Z")
@rtscott2001 Sure thing! Here’s the link: [https://agu.confex.com/agu/agu26/prelim.cgi/Session/279867](https://agu.confex.com/agu/agu26/prelim.cgi/Session/279867) ---
**Author:** ![rtscott2001](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/rtscott2001/32/5_2.png) [@rtscott2001](https://awg.osdr.space/u/rtscott2001)\ **Post date:** [July 13, 2026, 4:27pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/46 "2026-07-13T16:27:00Z")
Thank you so much! ---
**Author:** ![amanda](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@amanda](https://awg.osdr.space/u/amanda)\ **Post date:** [July 14, 2026, 3:59am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/47 "2026-07-14T03:59:29Z")
[@PlantAWG](https://awg.osdr.space/groups/plantawg) We’ll be having our 5th meeting on 7/16 (Thursday) at 7pm PST. We’ll work on our AGU abstract as well as provide updates for our current data analysis pipeline. Feel free to reach out if you have any questions. Hope to see you there! **Here is the meeting link: [PGC Subgroup Meeting #5](https://calendar.app.google/ZbahnkAM8nUCjkew8)** ---
**Author:** ![GasMan](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/gasman/32/2042_2.png) [@GasMan](https://awg.osdr.space/u/GasMan)\ **Post date:** [July 14, 2026, 6:53am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/48 "2026-07-14T06:53:52Z")
Hi everyone, I’ve been a bit quiet here, but I’ve been working on this in the background. Here’s a new Kaggle benchmark I’ve put together on NASA GeneLab’s OSD-120 Arabidopsis RNA-seq dataset. It’s called “OSD-120 Resilience Evaluation” and is designed to probe how well large language models can both plan and execute a realistic GLM-style RNA-seq workflow on spaceflight vs ground-control data. The benchmark has two tasks: - a hard execution task, where models must autonomously write and run Python code that ingests the OSD-120 AnnData object, fits an interaction model, and returns aligned outputs and interaction scores; - an easier JSON specification task, where models describe a complete OSD-120 resilience-analysis plan in structured JSON without running any code. By comparing these tasks, you can see where frontier models move from “nice biological language” to actually preserving biologically meaningful signal (including a curated set of 35 canonical genes) through the pipeline. The benchmark is backed by the NB01–NB06 notebook series that walks through the original OSD-120 analysis from root signal to pathway-level interpretation. kaggle Benchmark leaderboard and task descriptions: > **[OSD-120 Resilience Evaluation Leaderboard | Kaggle](https://www.kaggle.com/benchmarks/gastondana/osd-120-resilience-evaluation)** > > Benchmark evaluating LLMs on OSD-120 Arabidopsis RNA-seq. Models must autonomously clean data, perform GLM interaction modeling, and retrieve 35 canonical genes. Tests pipeline resilience and statistical fidelity in space-biology. Writeup (motivation, design choices, and how the rubric evolved): > **[OSD-120 Resilience Evaluation: Benchmarking LLMs on Space-Biology RNA-seq |...](https://www.kaggle.com/writeups/gastondana/osd120-resilience-evaluation)** > > A two-task benchmark on NASA GeneLab Arabidopsis RNA-seq that separates structured planning from real execution resilience. I’d be very interested in any feedback from the plant AWG on which aspects of the OSD-120 study you’d most like to see stressed in future versions (e.g., additional covariates, alternative contrasts, or different biological endpoints). I wanted to share this here before it circulates on social, since this group is closest to the underlying biology. I also have my ORCID tied to this R&D focus via a dedicated URL that should be live tomorrow. Do reach out if you have any questions. Thx! Gaston D. [@PlantAWG](https://awg.osdr.space/groups/plantawg) ---
**Author:** ![rtscott2001](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/rtscott2001/32/5_2.png) [@rtscott2001](https://awg.osdr.space/u/rtscott2001)\ **Post date:** [July 14, 2026, 7:05am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/49 "2026-07-14T07:05:25Z")
Could you join the next Plant AWG mtg and present this? ---
**Author:** ![GasMan](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/gasman/32/2042_2.png) [@GasMan](https://awg.osdr.space/u/GasMan)\ **Post date:** [July 14, 2026, 7:12am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/50 "2026-07-14T07:12:45Z")
I’ll try my best, my schedule is a bit unorthdox at the moment. However, Thursdays time frame should be fine. Worse case scenario, I plan to make a project walkthrough of what was going on my end during the testing period. It was very interesting data that I gathered in general whether it was input/output tokens, to the testing/exam questions, and tailoring the test/exam for the models due to consistent failures of actually understanding the source material I provided through the dataset and the NB01-NB06 series. Fascinating stuff all round. I’ll try to make it, I’ve been a night owl as of late, so Thursday should be fine. ---
**Author:** ![GasMan](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/gasman/32/2042_2.png) [@GasMan](https://awg.osdr.space/u/GasMan)\ **Post date:** [July 14, 2026, 11:20am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/51 "2026-07-14T11:20:33Z")
Morning, Just one more thing, I figured I’d share the OSD-120 Resilience Evaluation materials ahead of Thursday in case scheduling gets tight on my end. The project site has the benchmark overview, tasks, scoring rubric, and NB01–NB06 notebook lineage, and the slides walk through the main ideas and results. - Project site: [https://osd120-resilience-evaluation-site.vercel.app](https://osd120-resilience-evaluation-site.vercel.app) - Slides (walkthrough): [OSD-120 Resilience Evaluation - Google Slides](https://docs.google.com/presentation/d/1OFoz1XIr-1BaZiUMfLFDB50lS-wUcld6shcqpin5zP4/edit?usp=sharing) If I can’t join live, feel free to review these and send any questions, I’m happy to follow up async. There’s also a project navigator at the bottom which captures areas of the whole project and relays them back to you. Enjoy the Tuesday & rest of the week ahead, thx! ---
**Author:** ![rtscott2001](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/rtscott2001/32/5_2.png) [@rtscott2001](https://awg.osdr.space/u/rtscott2001)\ **Post date:** [July 14, 2026, 4:39pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/52 "2026-07-14T16:39:11Z")
You may want to share this also with @anna.lewkowicz & @james.casaletto in the Causal Inference subgroup of the [@AIMLawg](https://awg.osdr.space/groups/aimlawg) They are doing work on that specific dataset, iirc ---
**Author:** ![amanda](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@amanda](https://awg.osdr.space/u/amanda)\ **Post date:** [July 16, 2026, 5:18am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/53 "2026-07-16T05:18:17Z")
[@PlantAWG](https://awg.osdr.space/groups/plantawg) Reminder that our meeting is at 7pm (PST) tomorrow (7/16)! ---
**Author:** ![GasMan](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/gasman/32/2042_2.png) [@GasMan](https://awg.osdr.space/u/GasMan)\ **Post date:** [July 31, 2026, 11:51am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/54 "2026-07-31T11:51:33Z")
> [@Morgan\_Waltz](#): > > Has anyone done any research on those small Biospheres that people create in jars? There was this one guy that successfully made a small biosphere in a jar that has been sealed away for going on 30 years. Maybe for a sealed plant growth chamber it might need to mirror comparable to a mini-biosphere jar? Spit-balling here… > This is so exciting though!! Hi again @Morgan_Waltz Building on the mini-biosphere discussion, I put together a notebook review of a closed-jar system study ([Closed-Jar Burger Ecosystems-Day-2-Day Observation](https://www.kaggle.com/code/gastondana/closed-jar-burger-ecosystems-day-2-day-observation)) that highlights a key risk: thermal stress. When ambient cooling failed, the lack of an open-system buffer triggered a sharp heat spike inside the sealed jar, leading to a rapid collapse and complete die-off of internal life. Factoring in those microclimate temperature spikes seems critical when looking at the stability of sealed plant growth chambers. All the details are in the notebook, thought it might be an interesting data point for this! ---
**Author:** ![dr.richard.barker](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/dr.richard.barker/32/10_2.png) [@dr.richard.barker](https://awg.osdr.space/u/dr.richard.barker)\ **Post date:** [July 31, 2026, 7:57pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/55 "2026-07-31T19:57:28Z")
Interesting notebook, were those results pulled from the video? I liked the video too, i love how the “_Rollies pollies_” were one of the stars! Also, scary/important lesson about the potential devastating effect that heat shock can have on communities. ---
**Author:** ![GasMan](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/gasman/32/2042_2.png) [@GasMan](https://awg.osdr.space/u/GasMan)\ **Post date:** [July 31, 2026, 11:47pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/56 "2026-07-31T23:47:51Z")
Yes, the results were pulled from the video. I was just coding one day and came across the video on my feed, and thought to myself, why not. The video was a fun time! The rollie pollies must have hidden in the soil when he first placed the soil at the beginning of the video. Absolutely, that was the deciding factor in me taking the time to build out the notebook. The fact that they don’t have AC there and the heat wave hit his region, killing basically all of the organisms, if not close to all, was fascinating, as it could easily translate in other settings with heat spikes. Glad you took the time to watch the video and look over the notebook. I figured it was worth a share here. ---
**Author:** ![greenboxlabs](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/greenboxlabs/32/4404_2.png) [@greenboxlabs](https://awg.osdr.space/u/greenboxlabs)\ **Post date:** [August 13, 2026, 2:55am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/57 "2026-08-13T02:55:17Z")
This is a great problem to formalize. Separating a chamber-atmosphere artifact from a true microgravity response is exactly the kind of confounder that’s easy to lose in the transcriptomics if it isn’t pinned down in the metadata first. As GREENBOX Labs engineers the core growth chamber infrastructure for advanced plant research at leading institutions, harmonizing chamber-environment metadata is squarely in our wheelhouse. We’d be glad to help shape the atmosphere side of the harmonized table so datasets like EMCS (OSD-314) and CARA (OSD-120) stay comparable - and it lines up perfectly with the Hardware AWG SPLASH effort. Looking forward to it. Lisa ---
**Author:** ![amanda](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@amanda](https://awg.osdr.space/u/amanda)\ **Post date:** [August 18, 2026, 2:20am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/58 "2026-08-18T02:20:50Z")
This sounds super cool! Excited to have your interest, especially with the expertise in this topic ---
**Author:** ![amanda](https://avatars.discourse-cdn.com/v4/letter/a/67e7ee/32.png) [@amanda](https://awg.osdr.space/u/amanda)\ **Post date:** [August 18, 2026, 2:22am UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/59 "2026-08-18T02:22:35Z")
Sorry for the radio silence recently! After wrapping up our AGU submission, we are going to start working on adding to our pathway analysis by incorporating more datasets and plant chamber conditions. I’ll probably be sending out a whentomeet later this week! ---
**Author:** ![greenboxlabs](https://sea1.discourse-cdn.com/flex001/user_avatar/awg.osdr.space/greenboxlabs/32/4404_2.png) [@greenboxlabs](https://awg.osdr.space/u/greenboxlabs)\ **Post date:** [August 18, 2026, 3:34pm UTC](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926/60 "2026-08-18T15:34:19Z")
Thanks! Looking forward to contributing. [Previous page](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926.md?page=2) [Next page](https://awg.osdr.space/t/new-plant-growth-chamber-subgroup/3926.md?page=4)