Uni Münster Med. Fakultaet
IoB
NEWS
2024-06-13
"Application of a new data management system to the study of the gut microbiome of children who are small for their gestational age" by Manske et al. has been uploaded to bioRxiv.
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2024-06-07
"Interplay of miR-542, miR-126, miR-143 and miR-26b with PI3K-Akt is a Diagnostic Signal and Putative Regulatory Target in HPV-Positive Cervical Cancer" by Akram Rahimi-Moghaddam, Nassim Ghorbanmehr, Sedigheh Gharbi, Fatemeh Nili and Eberhard Korsching has been published by Biochemical Genetics
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2024-02
NewickTreeModifier: a simple web page to prune and modify Newick trees
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2023-08-28
"The complete sequence of a human Y chromosome” by T2T Consortium has been published by Nature
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2022-10-28
"The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research" by Felix Manske, Lynn Ogoniak, Norbert Grundmann and Wojciech Makalowski has been published by Nucleic Acids Research.
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2022-07-08
"A Map of 3' DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes" by Reza Halabian and Wojciech Makalowski has been published by Biology.
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2022-06
"paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences" by Lynn Ogoniak, Norbert Grundmann and others
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2022-05-14
"Mobilome of Apicomplexa Parasites" by Rodriguez and Makalowski has been published by Genes.
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2022-04-27
"Software evaluation for de novo detection of transposons" by Rodriguez and Makalowski has been published by Mobile DNA.
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2022-04-01
"From telomere to telomere: The transcriptional and epigenetic state of human repeat elements" by T2T consortium has been published by Science.
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2022-02-12
"Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing" by GRAID consortium that IoB is part of has been published by BMC Research Notes.
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Dipl. Inf. Norbert Grundmann
Norbert G
The biggest communication problem is we do not listen to understand - we listen to reply
To see more info - please select a topic of interest
I am responsible for soft- and hardware at this institute. You know, this is a never ending story and full of surprises. Previously I was working as an administrator at university, as a consultant and in an insurance company - mainly in software engineering and implementation. Much of my actual work belongs to genetic projects with the focus on software solutions for scientific questions.
As I started my work at this Institute I began to learn more about genetics and the underlaying software. For different projects I designed and implemented tools, like SCA for codon analsis and TinT for time evaluation of transpositions. A big project was and is the uorf database uORFdb. One thing that I have learned: software is only as good as the team that created it. Maybe we will work on the road together? :-)
I am very interested in the Unix System FreeBSD (and its neighbours like Open- and NetBSD) and happy that many of our servers are running BSD :-) I know *BSD needs sometimes more "hands-on", installation and background knowledge, but the result is a small, functional and stable system. Even on desktops! And it works!! :) I like this centric (but also community) approach very much. Even that I like and use *BSD systems I am not an enemy of others. But I think people, who claim that *BSD does not work, never took time to use it! I made experiences with Linux, Windows and OsX - and that is the reason why I switched completely to *BSD :) And by the way, there are many interesting operating systems available so far, which are very impressive and definitly worth to check them out - and maybe to switch over :) Following a table with these operating systems
FreeBSD FreeBSD is an operating system used to power modern servers, desktops, and embedded platforms. A large community has continually developed it for more than thirty years. Its advanced networking, security, and storage features have made FreeBSD the platform of choice for many of the busiest web sites and most pervasive embedded networking and storage devices.
GhostBSD GhostBSD provides a simple desktop-oriented operating system based on FreeBSD with MATE, OpenRC and OS packages for simplicity. GhostBSD has a selection of commonly used software preinstalled and required to start using it to its full potential.
hello helloSystem is a desktop system for creators with a focus on simplicity, elegance, and usability. Its design follows the "Less, but better" philosophy. It is intended as a system for "mere mortals", welcoming to switchers from the Mac. FreeBSD is used as the core operating system. Please refer to https://github.com/helloSystem/hello if you would like to learn more about the ideas and principles behind hello.
ravynOS ravynOS (previously called airyxOS) is an open-source operating system based on FreeBSD, CMU Mach, and Apple open-source code that aims to be compatible with macOS applications and has no hardware restrictions.
DragonFly BSD DragonFly belongs to the same class of operating systems as other BSD-derived systems and Linux. It is based on the same UNIX ideals and APIs and shares ancestor code with other BSD operating systems. DragonFly provides an opportunity for the BSD base to grow in an entirely different direction from the one taken in the FreeBSD, NetBSD, and OpenBSD series.
NetBSD NetBSD is a free, fast, secure, and highly portable Unix-like Open Source operating system. It is available for a wide range of platforms, from large-scale servers and powerful desktop systems to handheld and embedded devices.
OpenBSD The OpenBSD project produces a FREE, multi-platform 4.4BSD-based UNIX-like operating system. Our efforts emphasize portability, standardization, correctness, proactive security and integrated cryptography. As an example of the effect OpenBSD has, the popular OpenSSH software comes from OpenBSD.
HAIKU Haiku is an open-source operating system that specifically targets personal computing. Inspired by the BeOS, Haiku is fast, simple to use, easy to learn and yet very powerful.
Illumos illumos is a consolidation of software that forms the core of an Operating System. It includes the kernel, device drivers, core system libraries, and utilities. It is the home of many technologies include ZFS, DTrace, Zones, ctf, FMA, and more. We pride ourselves on having a stable, highly observable, and technologically different system. In addition, illumos traces it roots back through Sun Microsystems to the original releases of UNIX and BSD. see also OmniOS and openindiana.
ArcaOS Arca Noae brings OS/2 into the 21st Century
MorphOS MorphOS is a lightweight, highly efficient and flexible media-centric operating system.
MenuetOS MenuetOS is an operating system for PC, written fully in assembly language (64bit and 32bit). Features include pre-emptive and real-time multitasking with multiprocessor support and Graphical User Interface. Menuet64 is released under License and Menuet32 under GPL. Menuet supports both 64 and 32bit x86 assembly programming for smaller, faster and less resource hungry applications.
ReactOS Imagine running your favorite Windows applications and drivers in an open-source environment you can trust. That's the mission of ReactOS!
Qubes OS Qubes OS is a free and open-source, security-oriented operating system for single-user desktop computing. Qubes OS leverages Xen-based virtualization to allow for the creation and management of isolated compartments called qubes.
Redox Redox is a Unix-like Operating System written in Rust, aiming to bring the innovations of Rust to a modern microkernel and full set of applications.
OpenVMS VMS Software, Inc. is migrating OpenVMS and its layered products to the industry standard x86_64 architecture, to help customers protect their investment in OpenVMS infrastructure, especially in virtualized environments and in the cloud. OpenVMS E9.2 is available to all VMS Software, Inc. customers as their valuable feedback will contribute to the quality of the first production release, V9.2.
SerenityOS SerenityOS is a love letter to '90s user interfaces with a custom Unix-like core. It flatters with sincerity by stealing beautiful ideas from various other systems.
Chimera Linux A modern, general-purpose non-GNU Linux distribution. Chimera aims to be a clean and usable general-purpose Linux OS. In order to get there, it tries to liberate itself from the common baggage of most Linux-based systems and do its own thing. Software is sourced from different places and sometimes written from scratch. The FreeBSD tools were chosen for their high quality code and solid feature set. Some source code is also taken from NetBSD and OpenBSD. (nice!! :-))
KaOS Moving away from proprietary Operating Systems to open source options (Linux-based, BSD based, Solaris based) is about wanting freedom and choice in almost all cases. But should any such Operating System or Distribution not make some choices of what it believes is the best fit? KaOS sees a lack of focus in that respect. To create the highest quality Distribution possible, there needs to be a focus to make sure the user gets the best possible for whatever choice they made. It simply is not possible to package any and all to work perfect for every Desktop Environment or Toolkit.
My thoughts: Interesting that this product thinks about using using Illumnos kernel - woa! - away from pingiun based systems! I would like to test it :-) "though the Illumos kernel is under constant evaluation, and a future switch is a wish"
KolibriOS KolibriOS is a tiny yet incredibly powerful and fast operating system. This power requires only a few megabyte disk space and 8MB of RAM to run. Kolibri features a rich set of applications that include word processor, image viewer, graphical editor, web browser and well over 30 exciting games. Full FAT12/16/32 support is implemented, as well as read-only support for NTFS, ISO9660 and Ext2/3/4. Drivers are written for popular sound, network and graphics cards.
Syllable Welcome on the new web site for the Syllable operating system project. Syllable is a unique, modern and complete operating system that is easy to use, powerful, lightweight and extraordinarily fast and responsive. It has its own, tightly integrated kernel, file system, Graphical User Interface and applications, and also supports many cross-platform open-source programs. Syllable is designed in the tradition of the Amiga and BeOS, but built using many parts from the GNU project and Linux. It excels at interactive use. Syllable Server is a matching, small and efficient, companion Linux system. It uses the Linux kernel and is compatible with Linux software, but is otherwise built to be as similar as possible to the primary Syllable system. Syllable makes better use of your hardware by reducing waste in the software. It can make a new or tiny computer extremely fast and an old computer usable again.
AROS The AROS Research Operating System is a lightweight, efficient, and flexible desktop operating system, designed to help you make the most of your computer. It's an independent, portable and free project, aiming at being compatible with AmigaOS at the API level (like Wine, unlike UAE), while improving on it in many areas. The source code is available under an open source license, which allows anyone to freely improve upon it.
Friend OS Friend OS is a unique system that operates quite differently from the usual cloud-based setups. Instead of simply streaming or accessing a remote computer in the cloud, it does something fascinating. Here's how it works:
Imagine Friend OS as a versatile software system that you can use on your own device, like your smartphone or computer. It's not just a window into a distant computer; it's like having a whole new computer right there on your device.
Essence OS A desktop operating system built from scratch, for control and simplicity.
HelenOS HelenOS is a portable microkernel-based multiserver operating system designed and implemented from scratch. It decomposes key operating system functionality such as file systems, networking, device drivers and graphical user interface into a collection of fine-grained user space components that interact with each other via message passing. A failure or crash of one component does not directly harm others. HelenOS is therefore flexible, modular, extensible, fault tolerant and easy to understand.
And have a look on following stories
From Cloud Chaos to FreeBSD Efficiency
A few months ago, a client asked me to take care of their Kubernetes cluster (hosted on AWS and GCP). In their opinion, the costs were exorbitantly high for relatively simple and lean websites. Sure, they had many visits, but nothing too excessive development-wise.
I kindly declined. Unfortunately, their situation is all too common these days: they hired developers accustomed to working that way, convinced that a system administrator is now unnecessary because “the cloud has infinite potential.” They were used to considering optimization as secondary because “we have infinite power” (and this is already a spoiler for the ending).
Being open to dialogue and new experiences, they asked for my opinion on the matter. We talked for a while, and I explained that, in my view, for the type of setup they had (standard, with various replicas and variants, but primarily based on two platforms), it didn’t make sense. I saw it as complicating things. An over-engineering of something simple. Like taking a cruise ship to cross a river.
They then asked me to create something simple that would serve as a development server and for backups, to understand what kind of solution I had in mind.
User Friendly? GhostBSD vs Ubuntu - Download & Install
Interesting that installation of Ubuntu 24.04 did not to work, but GhostBSD 24.04 worked like a charm :-)
Case Study: Maintaining the World’s Fastest Content Delivery Network at Netflix on FreeBSD
For more than 25 years, Beckhoff Automation has used Windows as the exclusive operating system for its products. By adopting FreeBSD, they decreased their operating system footprint over sevenfold. Beckhoff came for FreeBSD's permissive license and stayed for its smaller footprint.
Ampere in the Wild: How FreeBSD Employs Ampere Arm64 Servers in the Data Center (Jan 2024)
FreeBSD vs Linux in 2022
Why (and how) we are migrating (many of) our servers from Linux to FreeBSD - it is new from Feb 2022!! :-)
Technical reasons to choose FreeBSD over GNU/Linux
So what is Linux - even if the founder does not like Debian or Ubuntu? - Why Linus Torvalds doesn't use Ubuntu or Debian
Linux != Linux?! Here a (more or less subjective) view from a Linux person: "Why Ubuntu is the Devil and Why So Many No Longer Use It"
A nice look back - I liked Solaris in much ways :) "OpenIndiana 2020.10d"
12 Reasons to Leave Windows, macOS or Linux - A Vocal Examination
The good old time :) SUN Ultra 24 - FreeBSD 13 & CDE
Deep Diving Into the Strengths of FreeBSD
MacOS to FreeBSD migration a.k.a why I left macOS
helloSystem: The "Less is More" FreeBSD Desktop
Another nice and new approach of an operating system: HAIKU - with some components based on FreeBSD
Android in FreeBSD bhyve by Oleg
NewickTreeModifier: a simple web page to prune and modify Newick trees
Comparison of circulating tumor cells and AR-V7 as clinical biomarker in metastatic castration-resistant prostate cancer patients
paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences
Presence of CTCs and its prognostic potential compared to AR-V7 expression in mCRPC undergoing androgen-deprivation therapy.
uORFdb - a comprehensive literature database on eukaryotic uORF biology
MetaGenomic analysis of short and long reads
GenoTypeMapper: graphical genotyping on genetic and sequence-based maps - published by Plant Methods
The multi-comparative 2-n-way genome suite - published in Genome Research
NanoPipe: a web server for nanopore MinION sequencing data analysis - published in GigaScience, giy169, doi: 10.1093/gigascience/giy169
GPAC - Genome Presence/Absence Compiler: A Web Application to comparatively visualize multiple genome-level changes - published in Oxford Journals
A Novel Web-Based TinT Application and the Chronology of the Primate Alu Retroposon Activity - published in BMC Evolutionary Biology
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Origin of the 1918 pandemic H1N1 influenza A virus as studied by codon usage patterns and phylogenetic analysis - published in Advance November 10, 2010, doi:10.1261/rna.2395211
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TEclass: a tool for automated classification of unknown eukaryotic transposable elements
2008 - now Design and implement biological software, setup and admininstrate Unix servers and external software at Institute of Bioinformatics (UKM) in Münster
2004 - 2007 Digitalize, store and provide access to incoming and outgoing letters. Write Java and PL/1 applications and connect host systems and Java environments at LVM in Münster
2000 - 2004 Consultant for Java applications in enterprise environments like CICS, IMS, MQ-Series at SerCon (now IBM) in Dortmund.
1994 - 2000 Study informatics at RWTH in Aachen.
1996 - 1998 Develop database applications for banks in Sybase/SQL at CsG in Aachen.
1994 - 1996 Administrator at Institute for Information Systems (I5) at RWTH in Aachen.
1990 - 1995 Design and implement retrival software in C (with database Progress and Interactive Unix) for tools like cutters and others used in industrial production at Cim Source GmbH in Aachen.
1987 - 1990 Training for "Mathematical Technical Assistent" at FH for Economy in Aachen.
1984 - 1985 Study physics at LMU in Munic.
2024-07-04 09:52