Katharina Hoff
@katharina_hoff
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Genome Annotation Geek, @uni_greifswald , always interested in friendly scientific collaboration, @KatharinaHoff @fosstodon .org, @katharinahoff .bsky.social
Greifswald, Germany
Joined September 2015
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Last Seen Profiles
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Tiberius brings accuracy towards a range where previous RNA-Seq or other extrinsic evidence was a must. Credits to the amazing team: Lars Gabriel, Felix Becker,
@Goemario
, all at
@uni_greifswald
Inspired by Helixer (by
@AlisandraDenton
), we explore the potential of deep learning for genome annotation. We introduce Tiberius for accurate ab initio prediction of protein coding genes in mammals. Tiberius beats Augustus, BRAKER3, and Galba.
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We are happy to present a preprint on BRAKER3, the pipeline for fully automated structural genome annotation with GeneMark-ETP, AUGUSTUS, and TSEBRA, using both RNA-Seq and protein database.
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A major change in the BRAKER genome annotation world: The GeneMark-Team changed the license of GeneMark (thank you so much!!!). There is no more need to install a license key file. Also GeneMark-ETP has improved stability due to their efforts.
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BRAKER v.3.0.0 release is now available. Docker container has been updated GeneMark-ETP is in the container. Best of luck! Team
@Goemario
+
@katharina_hoff
hope you can run BRAKER3, now!
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BRAKER v3.0.7 released. This version includes maximizing BUSCO completeness with compleasm (by
@csuhuangneng
) and documentation on a separate container for isoseq integration (with
@tomasbruna0
). More infos about this at
#PAG31
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Navigating Eukaryotic Genome Annotation Pipelines: A Route Map to BRAKER, Galba, and TSEBRA, a book chapter with
@tomasbruna0
and Lars Gabriel, now on arXiv:
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Excited to share our preprint on GALBA: Genome Annotation with Miniprot and AUGUSTUS
#EBP
#erga
Thanks a lot to
@tomasbruna0
@lh3lh3
@Goemario
& everyone else!
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Please, people who annotate genomes, there are no AUGUSTUS default parameters!!! Do not do this! You don't have tno always train AUGUSTUS but use parameters that fit to your species!
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BRAKER 3.0.8 is there. The main debugging for this release happened in Augustus and TSEBRA. One change is that the now containerize the latest Augustus instead of the debian package. You get all the updates if you pull the latest docker container.
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Our paper on GALBA for genome annotation with miniprot and AUGUSTUS is now available at BMC Bioinformatics. Very happy about the team that supports this project, had fun making it. Thanks
@tomasbruna0
@lh3lh3
@JosephGuhlin
team of
@Goemario
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I worked on visualizing the BRAKER and Galba inputs and their formats, today... sharing the fun.
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You are a bioinformatics expert in genome assembly and you are looking for a job? Rockefeller University has an interesting opening for you:
#bioinformatics
#job
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Being a woman in academia means for me first and most importantly to be a researcher and a teacher. But there are quirks. For example being a woman in academia with social media accounts means that I constantly worry about whether my profile pictures are appropriate. 1/n
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I am very happy today because I will meet some of the
@erga_biodiv
members. Will do my best to explain to you how to annotate eukaryotic genomes with BRAKER and TSEBRA 😁
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Want to know how to run BRAKER3 to predict genes? Sign up for one of our workshops now. It’s free.
We're up to 1680 signups and 1273 waitlists for
#Biodiversity
#Genomics
#Academy
!!
🤯
New sessions added on
- BRAKER3 gene prediction
- OMA/OMArk homology exploration and annotation QC
Check out to sign up
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@DalalSci
It is our job to train the next generation of scientists. And if they are talented, they often help a lot. We have several paper with our undergraduates as authors that would not have happened without them.
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We are excited about GALBA release v1.0.2 which has improved accuracy. Future improvements will follow!
@lh3lh3
@tomasbruna0
@Goemario
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It was really fun with you,
@erga_biodiv
. For everyone who wants to learn about using BRAKER & TSEBRA on their own, materials are available at (including instructions on how to run the docker container).
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Check out the new preprint on firefly genomes Great work with
@AnaGCatalan
and her colleagues.
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Totally worth retweeting, again. The teaching concept presented by the team of
@boas_pucker
is convincing.
"Life scientists benefit from (basic) programming skills"
#Bioinformatics
#OpenScience
#DataScience
#100DaysOfCode
#WomenWhoCode
#BigData
#MachineLearning
#serverless
#Linux
#Python
#coding
#SciComm
#PhdChat
#PhdLife
#Rstats
#Genomics
#WomenInSTEM
#edu
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Bye Czech Republic! The workshop
@evomics
at Cesky Krumlov was very cool, the railway system amazing, now looking forward to being home…
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Thx organizers of BGA23! It was my pleasure and now I will remain properly caffeinated, too! Amazing!
@sujaik
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„Stattdessen wird ein Bild des*der faulen Postdoc geschürt, der*die nur Leistung bringt, wenn genügend Druck aufgebaut wird und dessen Leistung die Mehrkosten einer Dauerstelle auf keinen Fall wett macht.“ Ein durchaus verbreitetes Bild. Macht mich immer wieder wütend.
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That feeling, you are almost there, almost at the preprint deposition and journal submission... exciting! Can't wait, it's a cool manuscript. Maybe another day or two...
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Power struggles in academia have substantially drained my batteries during the past months. I love my science, I love teaching. But it feels like there’s not much left of my energy for that because stereotypes persist in the academic system.
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@DB_Bahn
Nur aufs Klo geh ich unterwegs besser nicht. Gepostet aus der 1. Klasse RE Greifswald -> Berlin
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No gene prediction, no science. I am tweeting from my happy place, which is probably in any sunny & warm location with a decent swimming pool & my family. I really missed 50 m lanes at home. 😎🌞🏝️
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Looking forward to meeting bright scientists from all over Europe to practice structural genome annotation with BRAKER, GALBA, and TSEBRA, tomorrow.
#erga_biodiv
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We celebrate our wins! Honest congrats to everyone who just received a grant or an award. And we should communicate our losses because otherwise people who don’t receive a grant think they are losers. 2022: 2 denied. 2023: 2 granted. 2024: 1 denied. Shit happens.
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I appreciate that the annotation community picked up Galba and put it to work. However, using OrthoDB partitions as protein input is here not optimal. You miss evidence that you could easily have if you used full genome scale proteins of relatives.
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Looking forward to PAG in January! We will bring exciting news about BRAKER with different types and amounts of extrinsic evidence 😀
#genomeannotation
#bioinformatics
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I found this amazing preprint by
@EthanTolman
on bioarxiv, this morning. They describe a very simple and highly effective approach to increase the accuracy of GALBA gene sets. I implemented their approach in today's x-mas release of GALBA
Newly Sequenced Genomes Reveal Patterns of Gene Family Expansion in select Dragonflies (Odonata: Anisoptera)
#biorxiv_evobio
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Dear international colleagues, there’s a lot of information going around about a proposed change in Wissenschaftszeitvertragsgesetz in Germany. It is important that this was only a proposal. It has not been passed as a law, yet! We will do everything we can to prevent 1/n
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As a sports addict (though in bad shape since Covid), I am so used to the training effect: you try harder, the originally hard task becomes easier. In academia, I am still waiting for this effect to kick in 🤪
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Train station of Prague is amazing every single time that I pass through. It’s even heated! In Berlin, l‘d freeze miserably. Here, I am comfy with my winter coat, no freezing hands.
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Being a woman in academia makes me happy. But we have not solved all our problems, yet. Far from it.
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Being a woman in academia with a kid means continuously missing out on opportunities. Interesting talks and important networking events are scheduled in the evening. I can attend 20% of what I want to attend - thx to my supportive partner. 6/n
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I take this a reminder to our team to remove outdated protocols that linger on our web server.
My annual reminder to please stop using Tophat. Still papers using Tophat v1 (!) from 12 years ago 😱
There have been many better alternatives around for a long time now. Screenshot below is from
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Wenn Du in Greifswald wahlberechtigt bist: geh heute zum Bürgerentscheid! Gib rechtem Populismus keine Chance!
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Being a woman in academia means watching other women struggle with the system, watching many leaving. Brilliant women leave because working conditions in industries seem more appealing: permanent contracts, flexibility to advance, etc. 5/n
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Good news for University of Greifswald. Dedicated funding to promote women in science. It remains a long way to go…
Das Gleichstellungskonzept der
#UniGreifswald
wurde im Rahmen des Professorinnenprogramms 2030 positiv bewertet. Mit einer Förderung von 1.237.500 Euro wird die Unterstützung von Frauen in der Wissenschaft und die Parität an unserer Uni intensivieren.▶
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Being a woman in academia means being asked to join just about every committee that you can imagine. Ok, slight exaggeration. But you have to join a lot of administrative bodies because everyone wants gender balance but females are numerically underrepresented. 7/n
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I find this blogpost a little bizarre. It certainly lists important tools. But I never thought of BRAKER as a key feature of GeneMark. The MetAMOS authors may agree...
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Pacific A: Mark Borodvsky is walking us through history of GeneMark and the most recent GeneMark-ETP.
#PAG31
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Dear GALBA users, we at
@Goemario
team have made GALBA more secure for your file system by integrating Pygustus. The update is in the latest container, too. If you are a happy GALBA user, please let us know what kind of species you are using it for.
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It’s the first Saturday this year where I hear the birds singing at 5:30 am. love it!!!!! Spring is here :-)
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The University Hospital in Greifswald is looking to fill the position of an assistant professor in bioinformatics ("Juniorprofessur"). Please share this information.
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The Workshop on Genomics 2023 was super cool. I learned new things by browsing the slides and materials of others. Maybe you’ll like reading them, too..,
The Workshop on Genomics 2023 took place in a quaint little town in Czech Republic, for 2 weeks of an intense program. It successfully trained 70 early-career biologists from all around the world! Program:
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Looking much forward to this. It is possible to join spontaneously!
📣📣📣 Starting in 30 minutes!
Gene prediction with BRAKER3 -
with Katharina Hoff
@katharina_hoff
, who has been doing gene predictions since before I even knew what an intron was! :-)
Zoom Link at
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@lh3lh3
I agree. But I continue to teach students how to blow off their legs. (At least we dropped teaching Perl, change is possible.)
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@VeelaLaVeela
Danke für dieses Engagement! Habe u.a. Flüchtlinge in meiner Freizeit beim Schreiben von Bewerbungen unterstützt, das ist Aufwand. Die haben aber jetzt auch gute Jobs. Es braucht Menschen, die helfen. Eigentlich müsste das systematisch passieren.
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Being a woman in academia means that discussing “gendering” with male colleagues is a rather frequent experience. I am frankly quite sick of that. Address women as women, let’s be done with that, please 🙄. 4/n
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Sometimes, a day brings wonderful surprises. I am very grateful ❤️❤️❤️
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Welcome to the big leaves by the team of
@JillWegrzyn
is now published. Good read on genome annotation.
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Today, we presented and discussed preliminary results of the BMBF-funded project AI-Biome. With UMG, SensID GmbH and UG, we develop methods for early diagnostics of pathogens in dairy farms with NGS and AI.
#OneHealth
#AI
#NGS
#farming
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I am much looking forward to meet the workshop organizers and all participants in person, next week. Thank you for excellent organization!
The organizing team and TAs are already in Cesky Krumlov, getting everything ready for the Workshop on Genomics 2023! Looking forward meeting all the students on Sunday at the welcome reception!
#evomics2023
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@AmreiBahr
@FU_Berlin
@NW_mu_wi_schaft
Das Label familienfeindlicher Drittmittelgeber geht *Trommelwirbel* an das BMBF. Kostenneutrale Laufzeitverlängerung über das ursprüngliche Projektende hinaus nicht möglich. Voll super, wenn jemand Elternzeit nimmt 🙈
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My colleague Prof. Joscha Diehl is organizing an amazing spring school & workshop on "Mathematics of data streams: signatures, neural differential equations, and diffusion models" in Greifswald. Register at
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I read „The metamorphosis“ by Kafka in school (in German). It remains one of my favorites. I much enjoyed the ice sculptures exhibition in Rövershagen that this year has the topic „Metamorphosis“.
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I receive attention by men that I never asked for and that have nothing to do with science. Sent by complete strangers. Sometimes so bizarre and explicit that I escalate it through administration of my institution… learning that 2/x
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Dr. Ahmad Nazzal interviewed me for his science podcast. It was a pleasure to talk to you,
@nazzalisim
! I now in hindsight catch my own inaccuracies… see where I could have been more accurate 😉 But I hope people will enjoy to learn about our gene prediction research!
#science
Katharina Hoff: Gene Finding, Biotechnology, Diversity, Academia | Amd Lab Podcast # 8 (EN)
#Biotechnology
#podcasting
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Enjoying very much the talk by Anton Bankevich on assembly correctness. Very entertaining.
#PAG31
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@jlsteenwyk
@BinfoTrends
It’s an apples vs pears comparison… we say that in German. Hisat2 performs splice alignment. Answers are thus biased by the task frequency (bc bowtie & bwa don‘t).
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Genau deshalb müssen wir mehr als das Wissenschaftszeitvertragsgesetz ändern. Unbefristete Stellen im Mittelbau sind aktuell selten als „Karrieresprungbrett“ designed. (1/x)
Berufbarkeit ist Voraussetzung für Professur, nicht für unbefristete Stelle.
Argument, es brauche vor Entfristung genug Zeit, um Berufbarkeit zu erreichen, überzeugt daher nicht: Vermischt Stellentypen.
Erst entfristen, dann Berufbarkeit ermöglichen!
#WissZeitVG
#IchBinHanna
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@MicrobiomDigest
@FrontiersIn
Please one the authors must step forward and say this was just a prank. Pleaaaaaase.
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Another proposal submitted. Looking at the process of one proposal alone is easy. The overlay of many is just one big mess ;-)
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Very happy to share that the paper on the reference genome of sea star Pycnopodia helianthoides has been accepted for publication. Pleasure to have worked
@MNDlab
,
@LMSchiebelhut
&
@MelissaDeBiasse
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Es gibt Mittelbau-Stellen mit pi mal Daumen gleich viel Forschung und Lehre. In MV entspricht das Deputat hier exakt dem von Professuren. Die MA konkurrieren aber direkt mit Juniorprofs, Emmy Noether und Rückkehrer*innen aus dem Ausland (alles meist weniger Deputat). (3/x)
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Exactly! Ist nicht förderfähig… hab ich letzte Nacht wieder drüber gegrübelt.
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@AmreiBahr
Sieh es als Buffet der Möglichkeiten… der Teller ist immer zu voll. Noch eine Beschaffung hier, ein Gremienamt da, einen Schreibtisch dort hinstellen. Wie wir ans Buffet geraten sind, ist kein Geheimnis. A la carte wäre halt teurer.
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The structure of the tetraploid sour cherry 'Schattenmorelle' (Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature
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I go a long way to make meetings in the evening possible if there’s no other way because of time zone differences. That’s a good reason even for a late night meeting. But we are all in the same time zone and it f***ing 2024!
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A helpful blog article on Mastodon: an introduction for beginners and for scientists. – la bottega
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@jenniferhenkeHB
Diese “gezielte Ansprache” ist ein bizarres Konzept in D. Die BKs müssen dokumentieren, dass sie das soweit möglich machen - aber es bedeutet keineswegs, dass die BK oder Gutachter*innen des Verfahrens einen haben wollen. Empfinde ich mittlerweile als Zeitverschwendung.
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@OdedRechavi
Thank you!!! I was the one to stay at home with our kid, recently, while my husband chaired sessions at a conference that I would have liked to attend, too! We need childcare at conferences. Some provide. Most organizers don’t even think about it.
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I cannot stop laughing. This is so bad! Worth checking out the other images in that thread, too.
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@_baldanders
Ich wurde auch mal sehr belächelt, als ich mich in Jahr 3 nach der Promotion auf eine Juniorprofessur beworben habe. (Hat auch nicht geklappt, natürlich nicht!)
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We should celebrate women in STEM everyday, anyway 😉 Keep going
@gracegusta
!
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@StinaLindegren
Many in Germany start with 1470 Euros netto. This includes 2 hours teaching/week for many. On DFG grants, it’s mostly 1818, no teaching. It can be up to 2580, in computer science more common than in other areas. PhD stipends pay less.
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Wow. I am shocked. I do lots of committee duties. Some actually for fun, some to achieve gender balance. I had a feeling some male colleagues just dodge tasks, but it never occurred to me that it’s a systematic pattern.
A study on what many of us already know: over 75% of internal service work in academia is done by women. “We were surprised by how brazenly the male researchers described their priorities, for example that they actively didn’t respond to emails”
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Yes, please come see the downstairs posters at
#PAG31
! There are some really good ones downstairs!
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My colleague Stefan Simm (stefan.simm
@uni
-greifswald.de) is looking for a PhD student with a keen interest in AI (e.g. pytorch, tensorflow) and image as well as NGS analysis. If you are interested, I will be happy to e-mail you the full job description PDF. Nice Group!
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@CCWendling
I had it „almost happen“; got surprised by a submission confirmation from a journal. Contacted corresponding authors. Was an interesting conversation. Don’t really know what happened next (i.e. have not seen the paper appear but I may have missed it since it won’t be mine),
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When after a longer period of outside temperatures below zero associated with office temperatures around 16 the 18.6 degrees in your office seem so comfy & cosy… I love that dark and rainy winter weather right now! Emotions previously unknown…
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Posters and slides from
#PAG31
about BRAKER & GALBA are now in the docs folder of the respective software repositories (and also on Researchgate).
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How about an AI that takes my CV in PDF format and generates a DFG (German Research Association) compatible file? (Yes, I see the point of fairness with the mandatory template... but I have been staring at it for a couple of days, now, don't like to start.)
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Link:
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You need only one pipeline for structural genome annotation.
What unpopular academia opinion would get you in this situation?
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@RalphPordzik
@AmreiBahr
In anderen Ländern geht die Auswahl der Besten signifikant schneller und z.T. auch transparenter. NL: Bewerbung September, Ruf Dezember. NOR: Zusätzlich die Gutachten über alle Bewerber*innen. D macht das schon besonders schlecht.
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being a woman in academia means that others feel like they have to tell me to be careful, not to be on campus alone in late evenings, not to use backdoor exits. And they are probably right. Being a woman in academia means that I heed their advice. 3/n
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Traveling with
@DB_Bahn
from Greifswald to Berlin. Coincidentally even first class, and this is the bathroom. Piece of art, pearl of hygiene…
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@kapahi_pankaj
I received similar submissions (for a different task) from applicants. I put these candidates onto the „don’t proceed“ pile. Nothing wrong with using AI for the writing or coding process, in my opinion. But it doesn’t replace the thinking.
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Learn about OMA if you care about assessing annotation quality. OMA is the foundation of OMArk.
🌟 Ever heard of Hierarchical Orthologous Groups (HOGs)? They're clusters of orthologous genes representing different levels of evolutionary history. Stay tuned to learn more about their amazing potential! 🌍🐾
#HOGs
#Orthology
#Evolution
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