You know what sucks most in
#academia
?
It is when
#faculty
like us, want to hire highly talented candidates, and have the
#money
to provide a reasonable salary, but our institutional HR
#blocks
our offer cuz $$ we offered was too "high" considering the "number" of years of
Friendly reminder:
#Research
#Productivity
is not the same in every
#field
.
In some fields, students publish 10-30 pubs each year. In some fields, students publish 1 pub for their entire PhD. 1/n
Seq - a high-performance,
#Python
-based, compiled programming language geared toward
#biology
that combines the ease of use of high-level languages like Python or Matlab with the runtime performance of low-level languages like C or C++.
@Evilution84
Us
#PI
's job is not to convince our students to stay in
#academia
or move to
#industry
, or vice versa.
Our job is to present them
#options
to
#choose
, and be ready to answer the question - "What should I do if I want to be successful in [any area I want to be]"?
#AcademicChatter
We should implement at least one permanent
#Bioinformatics
#PI
position in each study section, same as
#biostatistics
.
We have been talking
#BigData
for over a decade, yet no recognization for the important role of
#Bioinformatics
scientists.
This makes me furious.
`gtsummary` + `flextable` saved me so much time and energy coding up clinical summary tables
tab1 <- tbl_summary(data.plot, by = Group)
tab1.print <- tab1 %>% as_flex_table()
save_as_docx(tab1.print,
path = 'tab1.docx')
done🤩
#Bionformatics
@_applechew
@AcademicChatter
First author papers are only expected if you plan to stay in academia & have your own lab. Needless to say, that is a narrow road. Lots of other great
#career
#choices
. The purpose of pursuing a
#PhD
is not papers, but to train your brain in order to be
#successful
in any career.
Spent 2.5 hours matching
#sample
#ids
from 5 different systems from 5 labs, named by 5 different teams, with 5 different naming conventions.
After some
#ninja
#skills
, only found 2 samples with unmatched ids across all 5 systems.
I call this a
#win
today 😂
#bioinformatics
As a huge
#introvert
, my default mode is to sit in the back seat , listen, smile, nod.
If I accumulate enough courage, sweep off my cold sweat, take a deep breath to make an announcement - I am not
#humblebrag
ing.
I am straight up
#bragging
. And it’s okay.
#AcademicChatter
- formalize a problem and solve it
- comprehend large amount of information in a short time
- quickly find recourses, learn new skills, master it
- understand failure is not the end, it is a process
- proficient programming in at least one language
#phdchat
#AcademicChatter
Challenge for
#PhD
people out there.
@AcademicChatter
Write down your top 5 transferable skills (yep, really. Write them down)
If you are anything like me, they will sound pretty generic and use buzz words like 'problem solving', 'critical thinking', 'communication'. 1/2
@GarmireGroup
Maybe not every weekend, but not unusual. Wet lab experiments are timed and if falls on weekends, one would have to come in (e.g. cell lines, animal exp, etc.). For folks in my lab, I encourage them to take another weekday off if they have to come in on weekends. 1/2
We really should show
#respect
to
#bioinformaticians
&
#biostatisticians
when they say "I spent a lot of time+effort trouble shooting this analytical code"
Same as when biologists say "I spent a lot of time+effort troubleshooting this experiment"
We really do.
#AcademicChatter
Paper accepted!!!!!!!!!!!!!
This is the first time Reviewers accepted our revisions after the 1st round 🥳 Thanks to The Editor and Reviewers for the constructive suggestions and comments!
Definitely encouraging news during the stressful grant submission time!
#AcademicChatter
Things I’ve learned after moving to a
#leadership
position:
1- some
#decisions
need to be made quick. Don’t drag.
2- most of time, providing a good enough
#answer
>>> spend days to come up w a perfect one (and it’s never perfect)
3-
#trust
is magical.
4- your
#time
is defined
@LisaMariaN91
never heard of it ... when I was in graduate school I went to lab on some weekends when I want my projects to move faster, but my PI never asked me to be there. Sometimes when I bumped into him on weekend in lab, he was like - WHY are you here don't you need sleep 😂
Protip
#Bioinformatics
#1
Saying no up front is 100x better than saying yes& not deliver.
#2
Build a network of whom you trust to work together is 100x fun than working alone.
#3
Team science is a double-edge sword. Be clear of your expectation from others, &others from you.
A collection of Excel tables != Databases
A collection of shell/R scripts != Pipelines
Fitting a line to data != AI
and
You don't need UMAP or t-SNE to visualize N=30 bulk samples
#Bioinformatics
@toomanyspectra
You are asking the right question, but to the wrong audience. The salary level is determined by university HR and funding agencies, not us faculty. In fact, even faculty wants to pay higher for their lab members, it gets rejected by HR and there is no mechanism to repeal.
Are you interested in
#bioinformatics
#DataScience
and enjoy collaboration with 400+ teams of scientists?
Join my team at
@UPMCHillmanCC
#Pittsburgh
!!
Position open:
We are looking for multiple candidates. DM me if you have any questions!!
Celebrate today. Not tomorrow. Not next month, or next year.
There will always be another grant, another paper, another project .
Happily placed a
#bubbletea
order for two 😎
..when I finish this paper
..when I submit that paper
..when I get this degree
..when I complete this task
..when I climb that ladder
..when I win this award
The future is always busy. Don't forget to live now.
This has happened too many in grants - when a grant is cut,
#bioinformatics
is the first to be cut. You end up still doing 50% of the work but only get paid 5%.
This will not change unless
#NIH
funds
#bioinformatics
as a separate discipline rather than an element of other grants.
In reality,
#good
#science
is
#slow
and often
#frustrating
. We have to repeat experiments to make sure obs is reproducible. We have to collect data to robustly test our hypothesis, to find something
#true
.
#Science
should not be rushed. Yet we are
#rushing
, all the time. 9/n
@jtleek
The most painful is not the experience but the time and effort spent on doing data
#cleaning
- which nobody values except the person who is doing it. All eyes and prizes on
#modeling
but data
#cleaning
and
#curation
is most critical gatekeeper on reliable signal inputs!
Major, real-time science rebuttals ongoing
#cancer
#microbiome
Within 48 hours after ground breaking reports shared on preprint, rebuttal, rebuttal of rebuttal, and rebuttal of rebuttal of rebuttal have been published
#code
&
#results
This is the best of
#ScienceTwitter
.🦠🔬👩🏻🔬
@GooglingBioinfo
If it’s raw data, start with basic Linux commands (sed, awk, etc.). Then find a tutorial and process a small set of data using Linux tools. If it’s processed data, start with basic R. Or, start with Python 🐍 , it’s a steeper climb but will be fun.
@saizhang0
Perfectly normal. One of the few opportunities in a year to take over the entire
#cluster
with zero
#queue
🤣 and no, it has nothing to do with life/work balance. As a PhD student, young and motivated, you do whatever you want to make your projects work.
#singlecell
twitter, recommendations on
#companies
who can take frozen cells and build 10x scRNAseq/scTCRseq/scBCRseq libraries? We had two failed runs during the past six months, and are exploring alternative options; before that all runs were great.
Any tips are welcome!! :)
On this very emotional moment when we are left w only 24h of a wonderful winter break b4 work starts again...
Did I accomplish writing goals? no
Did I re-train model and made it better? no
Did I finish analysis of 2m cells? also no
We cooked &rested together, that was it 🥳😂🥟
Super excited to
#share
on the 1st day of 2021, I published my first (of the last decade ever) personal website.
Check it out here 🥰🎉😈
#HappyNewYear2021
!!
@AdrianoAguzzi
I support everybody speaking their native tongue when having conversations amongst themselves.
#Inclusion
is not homogenous. It’s immigrants like us being comfortable speaking and sharing in a country where we were not born in.
Collaborators : would you like preprocessed data or raw data ?
Me: raw data please. Fresh out of the machine, no processing.
#Bioinformatics
#trustissues
😏
@drandersgs
@sridnona6
We did not use your results so we would not include you on paper.
Oh by the way thanks for sending all the results of that transcriptome assemblies, my PhD student used those sequences to run experiments.
@NinaSteele17
@mike_feigin
@Momademia
Find five senior , multi R01 funded PIs whom you trust, ask for 10 mins and present to them your hypothesis. If they don’t bite within first 1 min of your pitching , revisit your hypothesis, again, and again. Once the idea is solid, rest will flow.
@Nitasha__Sharma
@AcademicChatter
@OpenAcademics
Students should be free to reach out to professors and not be judged! Professors might not respond if too busy, but hash responses like that are not professional. On the plus side, that is a clear sign for students to screen out which labs *not* to join at the first place.
The moment when senior faculty recommends speakers, they start w ‘X has two R01s, would be a good candidate’. Or ‘X published xxx CNS papers, I recommend them’.
Shouldn’t we care more abt what we do to
#improve
#human
’s
#lives
, than specific metrics?
#AcademicChatter
#curecancer
@dgonzales1990
It's okay, I can assure you professional software developers might also have a hundred google tabs open.... sometimes it is equally important that you know where to find the answer, as knowing the answer yourself.
Thoughts on academic incentives. I am currently working on a program level grant with a core that's every bit as creative and involved as any of my grants as PI. But, the credit I will get should we win it will be way less.
Manually typed in 40+ author information on submission website
The moment you click submit, website is down for maintenance
I am done here
#AcademicChatter
and no, we do not do 5-mins heatmaps or 48-hour turnaround single cell results. Same as no PCR can be done within 5 mins, and no mouse experiments can be done within weeks, or sometimes months.
Recommendations for
#ultrafast
#splitting
fastq.gz into smaller files?
We have 100G WGS individual fastq.gz files; tried several tools, all single threaded and too slow, under a time crunch for grant submission 😱
The plan is splitting fq => bwamem => gatk chr
#Bioinformatics
After two weeks of almost no break, we decided to take a rest and finally relax. We made Cheese Buldak, Chinese sausage fried rice, and blueberry pancake 🥰
#weekendcooking
@AtienzarSara
it does not get easier, but you will develop strategies to manage it better. Most important is to build a support network to not feel alone :) grab coffee together and brainstorm ideas - always the most fun time as a PI!
#AcademicChatter
To
#survive
#academia
, find these five people
- a friend who shares your rants & joy
- an advisor who supports and points you the way
- a partner who you recede to and always feel safe
- a colleague who puts a stop to nonsense
- an inner yourself who is not afraid of anything
@conTaminatedsci
@GhadaHammad9
programming (the sort of class where you need to program in IDE on the fly in mid-terms/finals to pass) + probability (the sort of class where you need to do calculations on paper to pass) + linear algebra (yup calculations on paper too) will carry you a long way into science ...
5
#advice
I received that changed my life
- Guard your
#time
like guarding your bank account.
- The most
#successful
people are experts in saying, "No".
- Feeling angry is not productive. Find a
#solution
, then let go.
- Build a
#life
outside of career.
- Always set
#Priorities
.