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Invitation CompMS webinar Dr. Andy Lin – Challenges and applications of small databases in mass spectrometry-based proteomics data analysis
by BeNeLux bioinformaticians forum 19 Oct '23

19 Oct '23

Dear colleagues, We would like to invite you to an ISCBacademy<https://www.iscb.org/iscbacademy> webinar hosted by CompMS<https://compms.org/> and presented by Dr. Andy Lin (PNNL) on Monday, October 23 at 11:00 EDT / 17:00 CET. Challenges and applications of small databases in mass spectrometry-based proteomics data analysis The most common statistic for assigning statistical significance to peptide detections that result from a proteomics experiment is the false discovery rate (FDR). The FDR of a set of peptide-spectrum matches (PSMs) is typically estimated through a process called target-decoy competition, where spectra generated from a proteomics experiment are searched against a database of target and decoy sequences. This methodology is well adapted to most proteomics experiments, where the database is large or many proteins in the database are present in the sample. However, this methodology is challenged by small databases or when few peptides in the database are present in the sample. Recent advances, such as subset-neighbor search, aim to address to this challenge. Unfortunately, we show this approach fails for cases when the database is extremely small. In addition to discussing the unclear future of how to approach this scenario, we give several example applications that could utilize future solutions. You can join the webinar through the ISCB Nucleus<https://iscb.junolive.co/> platform. Feel free to share this information with any interested colleagues. Best, On behalf of CompMS, Wout, Timo, Lindsay, Isabell

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Empirical evaluations of large language models for bioinformatics education and research - ISCBacademy webinar, Thursday, November 9 at 11 am EDT
by BeNeLux bioinformaticians forum 17 Oct '23

17 Oct '23

Subject: Empirical evaluations of large language models for bioinformatics education and research - ISCBacademy webinar, Thursday, November 9 at 11 am EDT Dear all, The ISCBacademy webinar on Thursday, November 9 at 11 am EDT will be hosted by the ISCB Education COSI. Stephen Piccolo, from the Brigham Young University, will talk about “Empirical evaluations of large language models for bioinformatics education and research” (see the abstract below). You will find the information on how to connect at https://www.iscb.org/iscbacademy. You are most welcome to join us and spread the news among your colleagues. Kind regards, Patricia, Russell, and Wai Keat (ISCB Education COSI chairs) -- Abstract: Large language models (LLMs) have ignited great interest in the bioinformatics community. Many of us are interested in their potential uses (and misuses?) in research and education. The Piccolo Lab is undertaking empirical research to answer three such questions. 1) How well can LLMs translate human-language prompts into functional computer code? 2) How well can LLMs translate code snippets from one programming language to another? 3) How effectively can LLMs act as virtual assistants to students who are learning to write code? We have addressed each of these questions in the context of introductory bioinformatics and biostatistics education at the undergraduate level. In this seminar, I will describe our findings and discuss potential practical implications for education and research. -- [SIB logo] Patricia Palagi Head of Training SIB | Swiss Institute of Bioinformatics Quartier Sorge - Bâtiment Amphipôle - CH 1015 Lausanne - Switzerland t +41 21 692 40 78 Patricia.Palagi(a)sib.swiss<mailto:Patricia.Palagi@sib.swiss> - www.sib.swiss<http://www.sib.swiss> The information in this e-mail, and those ensuing, is confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, please destroy this message and notify the sender immediately.

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Join Our New Slack Community on Computational Mass Spectrometry
by BeNeLux bioinformaticians forum 11 Oct '23

11 Oct '23

Dear colleagues and fellow enthusiasts of computational mass spectrometry, As part of the CompMS<https://compms.org/> initiative, we are happy to share that we have launched an open Slack community dedicated to computational mass spectrometry, encompassing proteomics, metabolomics, and other fascinating applications. Our community will provide a space for: 1. Knowledge Sharing: Share your latest research findings, techniques, and insights in the field of computational mass spectrometry. Engage in discussions and exchange ideas with peers who share your enthusiasm. 2. Collaboration Opportunities: Discover potential collaboration partners, whether you are working on repository-scale analyses or other exciting projects. Forge connections that can drive your research forward. 3. Problem-Solving: Have a challenging problem or a question in your research? Our community is here to help. Tap into the collective wisdom of experts in the field. 4. Resource Exchange: Share valuable resources, tools, and software that can aid fellow members in their research endeavors. To join our Slack community, please use this invitation link<https://join.slack.com/t/compms/shared_invite/zt-24neur6wz-gu2KmKAnWcDAWspC…>, and feel free to share this further. We look forward to seeing you on Slack. If you have any questions or suggestions, please feel free to reach out to me directly or through Slack. Thank you for being a part of this exciting venture, and let's work together to push the boundaries of computational mass spectrometry! Best, On behalf of CompMS, Wout

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LAST CHANCE for early birds: BioSB course "Integrated Modeling and Optimization"
by BeNeLux bioinformaticians forum 11 Oct '23

11 Oct '23

Dear Colleagues, Please note, there are still four days to register at an early-bird reduced rate for the BioSB course: Integrated Modeling and Optimization<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…> Wageningen, 11 - 15 December 2023 (early bird fee until October 16) What it's about? In validating models one always meet with the need to fit models to data. So, the parameters that are present in any realistic model have to be chosen based on comparison of model predictions with data. In this matching process optimization techniques are indispensable. That’s why a considerable part of this course is spent on getting you acquainted with the optimization techniques that are nowadays available and widely used. Numerical optimization also is the basis for so-called flux balance analysis (FBA), commonly used to study large metabolic networks. This type of models and their analysis and simulation is also introduced in the course. More information and registration: click here<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…>. We look forward to welcoming you. Kind regards, Petra Aarnoutse Community manager BioSB [cid:part1.c5aevw0a.AiUrJ7j9@health-RI.nl]

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Junior Lecturer Bioinformatics and Systems Biology VU/UvA master’s programme
by BeNeLux bioinformaticians forum 10 Oct '23

10 Oct '23

Dear all, We have are again hiring junior lecturer to strengthen the bioinformatics teaching team within the VU/UvA joint degree master programme Bioinformatics & Systems Biology in Amsterdam. For details and application procedure, please see https://werkenbij.vu.nl/ad/junior-lecturer-juniordocent-masters-programme-b… -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1111 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +312059 87783 - skype: kafeenstra - room NU 12A31| | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | | | "If we knew what it was we were doing, it would not | | | be called research, would it?" (Albert Einstein) | |_____________|_______________________________________________________| _______________________________________________ BBClist mailing list BBClist(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/bbclist

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job vacancy Project Lead Artificial Intelligence
by BeNeLux bioinformaticians forum 09 Oct '23

09 Oct '23

Dear Sirs, Could you please share the vacancy below with the mailing list? *Project Lead Artificial Intelligence* *Job objective * Our organization keeps moving. This results in a fast-changing and, therefore, challenging environment. As a Project Lead Artificial Intelligence and Data Science you strengthen the R&D Trait Genetics group. With your solid background in bioinformatics you lead projects, work packages and activities on the design of algorithms and pipelines using high throughput phenotyping methods like imaging data. You translate these pipelines into solutions for our global breeding and research programs. In addition, you are responsible for setting up, developing and maintaining the IT solutions for our Trait Genetics team. Collaboration is key for this job position. You will work closely with breeders and scientists from different backgrounds (including bioinformatics, biology, genetics, phytopathology and trait discovery) to develop tailored solutions that meet their needs. You will report to the Technology Lead Trait Genetics in the Breeding Technology Centre in De Lier. *Your tasks and responsibilities* · Design, improve and maintain innovative software solutions for large data challenges within the global Dümmen Orange R&D portfolio. · Initiate and lead work packages and projects on developing pipelines for computer vision (preprocessing, segmentation, machine learning, deep learning, etc), which feed into genomic analyses and molecular breeding applications. · Deploy software tools and pipelines for routine breeding application through automation or for end-users through web-apps or Notebooks. · Perform scouting activities for novel tools and technologies. · Design, improve and maintain IT infrastructure and solutions for our Trait Genetics team. · Build and maintain an internal and external network of collaborations. · Provide functional and organizational leadership. *Your profile* · PhD in a relevant field in computer science or biology with a strong computational focus (for example bioinformatics, data science) and preferably >2 years experience in industry. · You have a thorough understanding of the Linux operating system and are proficient in coding in Python and R (other programming languages are nice to have). - Proven experience in advanced computer vision applications preferably using various deep learning approaches (for example for object detection and segmentation). - Proven experience in analyzing large datasets and data visualization. · Experience with DevOps (Kubernetes, Docker), databases (SQL), workflow management (Airflow) and cloud computing (Azure) is desirable. · Experience with front-end development (Dash, Pyscript, Rshiny) is desirable. - Prior knowledge of biology is not essential, but affinity with plant breeding and quantitative genetics is desirable. · Ability to work independently as well as in fast-paced multidisciplinary teams. · Inquisitive, innovative and critical mind-set and a creative and pro-active attitude. · Ability to communicate across disciplines and functions. · Excellent command of English and willingness to learn Dutch. Vancy can be found online on : https://emea.dummenorange.com/site/nl/vacatures/detail?job=project-lead-art… *Camillo Berenos*

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[bioinfo] CMSB 2022: call for participation
by BeNeLux bioinformaticians forum 09 Oct '23

09 Oct '23

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Vacancy: PhD position in computational single-cell cancer biology
by BeNeLux bioinformaticians forum 04 Oct '23

04 Oct '23

Dear all, For an exciting project using state-of-the-art single cell measurements to elucidate the interplay between cell state and drug response in cancer we are looking for an enthusiastic PhD candidate with a strong quantitative background. The position is shared between the groups of Lodewyk Wessels (NKI) and Evert Bosdriesz (VU). Deadline for application is October 22. More information in the link. https://werkenbij.vu.nl/ad/phd-kwf-cell-state-dependent-drug-response/mq7m4j Kind regards, Evert Bosdriesz ---- Assistant Professor Bioinformatics - VU Amsterdam www.evertbosdriesz.org<http://www.evertbosdriesz.org> | e.bosdriesz(a)vu.nl<mailto:e.bosdriesz@vu.nl>

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BioSB news - courses and events
by BeNeLux bioinformaticians forum 27 Sep '23

27 Sep '23

Dear all, The BioSB research school is happy to invite you to the HotTopic Symposium: Computational Methods for (single cell) Spatial Data Analysis<https://www.dtls.nl/events/biosb-hottopics-symposium-computational-methods-…> – LUMC Leiden, 17 November 2023 (Free entrance after registration) BioSB and ‘single cell network Netherlands’ (scNL) are co-organising this symposium. The goal of this informal meeting is to bring together people who are interested in this topic in order to learn about the latest development, and to build a community. For more information click here. <https://www.dtls.nl/events/biosb-hottopics-symposium-computational-methods-…> BioSB also announces that registration is open for BioSB course: Integrated Modeling and Optimization<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…> - Wageningen, 11 - 15 December 2023 (early bird fee till October 16) In validating models one always meet with the need to fit models to data. So, the parameters that are present in any realistic model have to be chosen based on comparison of model predictions with data. In this matching process optimization techniques are indispensable. That’s why a considerable part of this course is spent on getting you acquainted with the optimization techniques that are nowadays available and widely used. Numerical optimization also is the basis for so-called flux balance analysis (FBA), commonly used to study large metabolic networks. This type of models and their analysis and simulation is also introduced in the course. For more information click here<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…>. Last but not least: please mark your calendars and SAFE THE DATE for The BioSB 2024 conference: 18 - 19 June 2024, Egmond aan Zee, NL. More information will follow soon! We hope to see many of you at one of the BioSB events and courses. Be welcome! Best regards, Petra Aarnoutse BioSB community manager [cid:part1.pLKCtXnZ.4aYrC2St@health-RI.nl]

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Open Positions - BioMed X, Germany
by BeNeLux bioinformaticians forum 25 Sep '23

25 Sep '23

Hello, My name is Bianca, and I am the Recruiting & Communications Manager at the BioMed X Institute<https://bio.mx/>, in Heidelberg, Germany. We have two open positions in one of our research teams - Team VPE<https://bio.mx/research-teams/artificial-intelligence/team-vpe/>, Virtual Patient Engine - to be filled out by researchers with expertise in machine learning/AI and bioinformatics. Would it be possible for you to advertise these two positions? We would be very grateful for your help. Here are the links, let me know if you require more information (or if the information needs to be in a different format): 1) Bioinformatician Position at BioMed X<https://atpscan.global.hornetsecurity.com/index.php?atp_str=kpHUHng3sjeHbfj…> 2) Algorithm Researcher Position at BioMed X<https://atpscan.global.hornetsecurity.com/index.php?atp_str=EspSwRYAmgFUwDv…> Thank you very much! Best wishes, Bianca --------------------------------------------------- Flavia-Bianca Cristian PhD Recruiting & Communications Manager [cid:image001.jpg@01D9EFBF.4A084BF0] BioMed X GmbH Im Neuenheimer Feld 515 69120 Heidelberg, Germany Tel.: +49 6221 426 11 706 Mobile: +49 172 7540707 E-Mail: fbc(a)bio.mx<mailto:fbc@bio.mx> ----------------------------------------------------------------------------------------- Principal Office: Heidelberg Commercial Register: Mannheim, HRB 716390 Managing Director: Dr. Christian Tidona Chairman of the Supervisory Board: Dr. Gerhard Ries -----------------------------------------------------------------------------------------

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