How ChatGPT excels & fails in writing Bioinformatics code, grants and tutorials

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Can't keep up with all the interesting #ChatGPT prompts? Nothing to worry about! I curated a 🧵for you with key messages & relevant tweets on where our new academic companion #ChatGPT excels or fails in writing #Bioinformatics code, academic grants & tutorials👇

1. Our new friend is very good with writing #Python and #RStats code. 1.1 Here, it teaches us plotting with pandas & matplotlib, together with explanatory text. If you are in the process of learning/improving your Python skills, #ChatGPT is of real help. twitter.com/goodside/status/1598235521675038722?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.2 It is amazing that it can also debug code really well. It finds bugs, explains them, then fixes them! twitter.com/amasad/status/1598042665375105024?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.3 It explains what complicated regex expressions mean, a task that can be hard and time-consuming to backtrack on Google. Also not fun for most folks. twitter.com/jwblackwell/status/1598090447854792705?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.4 Here's a helpful starting point for genomic analyses: @tangming2005's suggestion for a snakemake routine to preprocess genomics data and get some (hopefully meaningful) output. twitter.com/tangming2005/status/1599583280319188992?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.5 However, hold off your excitement (or worry) for a second. Not all genomics data scientists are out of jobs (at least not yet). twitter.com/kieranrcampbell/status/1598865069101940736?s=20&t=bAPwcOrgU1hecvTiPFVJSg

1.6 One of my favorites! We already have an #RStats package that can put #ChatGPT's skills to good use for plotting, live from RStudio. twitter.com/IsinAltinkaya/status/1599440535529623552?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.7 Another cool one! You can build an R Shiny app in few minutes, by writing no code. Honestly, it's hard for me to see how all these examples cannot be of real utility to data scientists. twitter.com/jfernandez__/status/1599470590405976064?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.8 Yet one more quick & useful #RStats application twitter.com/tanyacash21/status/1599425382817464320?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.9 Helpful tip wen using it to support your coding: it can also update its previously written #RStats code, and improve its syntax. twitter.com/dr_keithmcnulty/status/1599716570569138177?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.10 On a different, but really important note, it can help with your deepest git-related questions. Very useful for #DataScience and #Bioinformatics folks, as nowadays GitHub repos are the most popular way to distribute research code. twitter.com/tylerangert/status/1598389755997290507?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

1.11 Lastly, I found this to be truly impressive and educational: solving complex programming puzzles with code. Very useful for talented maths/CS school students. twitter.com/ahmetb/status/1599637948051652609?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

2. Now on to more research-like tasks. 2.1 #ChatGPT can also code simple mathematical models, and explain what they mean. In general, best success for more complex tasks is insisting with follow-up questions, which help it improve its outputs. twitter.com/marcelsalathe/status/1598769656776384512?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

2.2 I found Lior's one to be pretty impressive @lpachter. Not only the proposed code to test one of the most famous unsolved conjectures in maths was correct, it also just ran on Google Colab. twitter.com/lpachter/status/1599623200530640897?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

2.3 However, beware, it can also screw up basic concepts and questions, which are essential for the vast majority of Data Science analyses. Take-home message here: don't trust it blindly (at least not yet). twitter.com/doctorveera/status/1599567073889308673?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

3. Our new friend is also very good with academic writing. 3.1 Finding the right LaTeX syntax for math formulas can be time-consuming. #ChatGPT seems to curate this information well. twitter.com/jdjkelly/status/1598021488795586561?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

3.2 Writing essays on given topics (e.g. for grant introduction purposes). Topics can range from very popular to really niched. twitter.com/corry_wang/status/1598176074604507136?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

3.3 Grant writing is one of #AcademicTwitter's favorite automation candidates (I wonder why) twitter.com/SScottGraham_/status/1599118981591621632?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

3.4 I mean it, people have tried it in many different ways and it's actually overall not that bad. twitter.com/MarkBoukes/status/1598298494024159232?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

3.5. Even paper intros are not that bad, given that this all only takes few seconds to write. Not that bad. twitter.com/anobelodisho/status/1598715564603899909?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

3.6 Still, watch out and don't take everything it says too seriously😀. Making up reference articles in papers and grant proposals (and nowhere, actually) is not that fun. twitter.com/marcelsalathe/status/1598184404366790658?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

3.7 Teaching and setting up tutorials can be less time consuming moving forward, if you make good use of #ChatGPT's abilities. twitter.com/RobLanfear/status/1599495864976027648?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

4. Some people believe our new friend will replace Dr. Google. Not sure about that, but I agree Dr. Google is a pretty low bar. twitter.com/RoxanaDaneshjou/status/1598170660186251264?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

5. Our new friend is also very creative. Poems are his definitely his/her thing. 5.1 Really likes making fun of postdocs and being painfully accurate in doing so. twitter.com/raphaelmilliere/status/1598469100535259136?s=20&t=YceWcSRQX0-A3usum7M85w

5.2 Also got a pretty good understanding of long-read DNA sequencing. twitter.com/grahamserwin/status/1598801904020164608?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

6. Too good to be true? Many people have summarized their #ChatGPT prompts into thoughtful threads with recommendations on which general tasks are better suited for success, and which are less so. twitter.com/ChristophMolnar/status/1599707850229841920?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

On the same line of thought, good to keep in mind that the scientific process requires real self-reflection and cognitive ability. Our new friend has still a long way to travel to get there. Good to keep perspective. twitter.com/Michael_J_Black/status/1598206216525725697?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg

Last tweet is a bonus, for everybody who needs to give a quick answer as to what they've been doing the whole week, when in fact they did nothing. The future looks bright!🌞 twitter.com/goodside/status/1599082185402642432?s=20&t=C7SsnqfyVf-zW3BsEv_Ytg