@inproceedings{FranzSaathoffGorlitzetal.2006, author = {Franz, Thomas and Saathoff, Carsten and Gorlitz, Olaf and Ringelstein, Christoph and Staab, Steffen}, title = {SEA: A Lightweight and Extensible Semantic Exchange Architecture}, series = {2nd Workshop on Innovations in Web Infrastructure. 15th International World Wide Web Conference, Edinburgh, Scotland}, booktitle = {2nd Workshop on Innovations in Web Infrastructure. 15th International World Wide Web Conference, Edinburgh, Scotland}, address = {Edinburgh}, organization = {CiteSeerX}, pages = {1 -- 7}, year = {2006}, language = {en} } @inproceedings{FranzSaathoffGoerlitzetal.2006, author = {Franz, Thomas and Saathoff, Carsten and G{\"o}rlitz, Olaf and Ringelstein, Christoph and Staab, Steffen}, title = {SEA: Introducing the Semantic Exchange Architecture}, series = {Demos and Posters of the 3rd European Semantic Web Conference (ESWC 2006), Budva, Montenegro, 11th - 14th June, 2006}, booktitle = {Demos and Posters of the 3rd European Semantic Web Conference (ESWC 2006), Budva, Montenegro, 11th - 14th June, 2006}, address = {Budva}, url = {http://nbn-resolving.de/Poster}, year = {2006}, language = {en} } @inproceedings{FranzStaabArndt2007, author = {Franz, Thomas and Staab, Steffen and Arndt, Richard}, title = {The X-COSIM integration framework for a seamless semantic desktop}, series = {Proceedings of the 4th international conference on Knowledge capture}, booktitle = {Proceedings of the 4th international conference on Knowledge capture}, editor = {Sleeman, Derek and Barker, Ken}, publisher = {ACM}, address = {New York, NY}, isbn = {978-1-59593-643-1}, doi = {10.1145/1298406.1298433}, pages = {143}, year = {2007}, language = {en} } @article{HuberSchnaussRoenickeetal.2013, author = {Huber, Florian and Schnauß, J{\"o}rg and R{\"o}nicke, S. and Rauch, P. and M{\"u}ller, K. and F{\"u}tterer, C. and K{\"a}s, Josef}, title = {Emergent complexity of the cytoskeleton: from single filaments to tissue}, series = {Advances in Physics}, volume = {62}, journal = {Advances in Physics}, number = {1}, publisher = {Taylor \& Francis}, issn = {1460-6976}, doi = {10.1080/00018732.2013.771509}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34812}, pages = {1 -- 112}, year = {2013}, abstract = {Despite their overwhelming complexity, living cells display a high degree of internal mechanical and functional organization which can largely be attributed to the intracellular biopolymer scaffold, the cytoskeleton. Being a very complex system far from thermodynamic equilibrium, the cytoskeleton's ability to organize is at the same time challenging and fascinating. The extensive amounts of frequently interacting cellular building blocks and their inherent multifunctionality permits highly adaptive behavior and obstructs a purely reductionist approach. Nevertheless (and despite the field's relative novelty), the physics approach has already proved to be extremely successful in revealing very fundamental concepts of cytoskeleton organization and behavior. This review aims at introducing the physics of the cytoskeleton ranging from single biopolymer filaments to multicellular organisms. Throughout this wide range of phenomena, the focus is set on the intertwined nature of the different physical scales (levels of complexity) that give rise to numerous emergent properties by means of self-organization or self-assembly.}, language = {en} } @article{HuberRidderVerhoevenetal.2021, author = {Huber, Florian and Ridder, Lars and Verhoeven, Stefan and Spaaks, Jurriaan H. and Diblen, Faruk and Rogers, Simon and van der Hooft, Justin J. J.}, title = {Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships}, series = {PLOS Computational Biology}, volume = {17}, journal = {PLOS Computational Biology}, number = {2}, publisher = {Cold Spring Harbor Laboratory}, organization = {PLOS}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1008724}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34687}, year = {2021}, abstract = {Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm-Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds.}, language = {en} } @article{SchornVerhoevenRidderetal.2021, author = {Schorn, Michelle A. and Verhoeven, Stefan and Ridder, Lars and Huber, Florian and Acharya, Deepa D. and Aksenov, Alexander A. and Aleti, Gajender and Moghaddam, Jamshid Amiri and Aron, Allegra T. and Aziz, Saefuddin and Bauermeister, Anelize and Bauman, Katherine D. and Baunach, Martin and Beemelmanns, Christine and Beman, J. Michael and Berlanga-Clavero, Mar{\´i}a Victoria and Blacutt, Alex A. and Bode, Helge B. and Boullie, Anne and Brejnrod, Asker and Bugni, Tim S. and Calteau, Alexandra and Cao, Liu and Carri{\´o}n, V{\´i}ctor J. and Castelo-Branco, Raquel and Chanana, Shaurya and Chase, Alexander B. and Chevrette, Marc G. and Costa-Lotufo, Leticia V. and Crawford, Jason M. and Currie, Cameron R. and Cuypers, Bart and Dang, Tam and de Rond, Tristan and Demko, Alyssa M. and Dittmann, Elke and Du, Chao and Drozd, Christopher and Dujardin, Jean-Claude and Dutton, Rachel J. and Edlund, Anna and Fewer, David P. and Garg, Neha and Gauglitz, Julia M. and Gentry, Emily C. and Gerwick, Lena and Glukhov, Evgenia and Gross, Harald and Gugger, Muriel and Guill{\´e}n Matus, Dulce G. and Helfrich, Eric J. N. and Hempel, Benjamin-Florian and Hur, Jae-Seoun and Iorio, Marianna and Jensen, Paul R. and Kang, Kyo Bin and Kaysser, Leonard and Kelleher, Neil L. and Kim, Chung Sub and Kim, Ki Hyun and Koester, Irina and K{\"o}nig, Gabriele M. and Leao, Tiago and Lee, Seoung Rak and Lee, Yi-Yuan and Li, Xuanji and Little, Jessica C. and Maloney, Katherine N. and M{\"a}nnle, Daniel and Martin H, Christian and McAvoy, Andrew C. and Metcalf, Willam W. and Mohimani, Hosein and Molina-Santiago, Carlos and Moore, Bradley S. and Mullowney, Michael W. and Muskat, Mitchell and Nothias, Louis-F{\´e}lix and O'Neill, Ellis C. and Parkinson, Elizabeth I. and Petras, Daniel and Piel, J{\"o}rn and Pierce, Emily C. and Pires, Karine and Reher, Raphael and Romero, Diego and Roper, M. Caroline and Rust, Michael and Saad, Hamada and Saenz, Carmen and Sanchez, Laura M. and S{\o}rensen, S{\o}ren Johannes and Sosio, Margherita and S{\"u}ssmuth, Roderich D. and Sweeney, Douglas and Tahlan, Kapil and Thomson, Regan J. and Tobias, Nicholas J. and Trindade-Silva, Amaro E. and van Wezel, Gilles P. and Wang, Mingxun and Weldon, Kelly C. and Zhang, Fan and Ziemert, Nadine and Duncan, Katherine R. and Cr{\"u}semann, Max and Rogers, Simon and Dorrestein, Pieter C. and Medema, Marnix H. and van der Hooft, Justin J. J.}, title = {A community resource for paired genomic and metabolomic data mining}, series = {Nature Chemical Biology}, volume = {17}, journal = {Nature Chemical Biology}, number = {4}, publisher = {Nature}, issn = {1552-4469}, doi = {10.1038/s41589-020-00724-z}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34708}, pages = {363 -- 368}, year = {2021}, language = {en} } @article{AdamatzkySchnaussHuber2019, author = {Adamatzky, Andrew and Schnauß, J{\"o}rg and Huber, Florian}, title = {Actin droplet machine}, series = {Royal Society Open Science}, volume = {6}, journal = {Royal Society Open Science}, number = {12}, publisher = {Royal Soc. Publ.}, issn = {2054-5703}, doi = {10.1098/rsos.191135}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34675}, year = {2019}, abstract = {The actin droplet machine is a computer model of a three-dimensional network of actin bundles developed in a droplet of a physiological solution, which implements mappings of sets of binary strings. The actin bundle network is conductive to travelling excitations, i.e. impulses. The machine is interfaced with an arbitrary selected set of k electrodes through which stimuli, binary strings of length k represented by impulses generated on the electrodes, are applied and responses are recorded. The responses are recorded in a form of impulses and then converted to binary strings. The machine's state is a binary string of length k: if there is an impulse recorded on the ith electrode, there is a '1' in the ith position of the string, and '0' otherwise. We present a design of the machine and analyse its state transition graphs. We envisage that actin droplet machines could form an elementary processor of future massive parallel computers made from biopolymers.}, language = {en} } @article{AdamatzkyHuberSchnauss2019, author = {Adamatzky, Andrew and Huber, Florian and Schnauß, J{\"o}rg}, title = {Computing on actin bundles network}, series = {Scientific Reports}, volume = {9}, journal = {Scientific Reports}, number = {1}, publisher = {Springer Nature}, issn = {2045-2322}, doi = {10.1038/s41598-019-51354-y}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34665}, year = {2019}, abstract = {Actin filaments are conductive to ionic currents, mechanical and voltage solitons. These travelling localisations can be utilised to generate computing circuits from actin networks. The propagation of localisations on a single actin filament is experimentally unfeasible to control. Therefore, we consider excitation waves propagating on bundles of actin filaments. In computational experiments with a two-dimensional slice of an actin bundle network we show that by using an arbitrary arrangement of electrodes, it is possible to implement two-inputs-one-output circuits.}, language = {en} } @article{MiguelesRowlandsHuberetal.2019, author = {Migueles, Jairo H. and Rowlands, Alex V. and Huber, Florian and Sabia, S{\´e}verine and van Hees, Vincent T.}, title = {GGIR: A Research Community-Driven Open Source R Package for Generating Physical Activity and Sleep Outcomes From Multi-Day Raw Accelerometer Data}, series = {Journal for the Measurement of Physical Behaviour}, volume = {2}, journal = {Journal for the Measurement of Physical Behaviour}, number = {3}, publisher = {Human Kinetics}, issn = {2575-6605}, doi = {10.1123/jmpb.2018-0063}, pages = {188 -- 196}, year = {2019}, language = {en} } @article{BeniddirKangGentaJouveetal.2021, author = {Beniddir, Mehdi A. and Kang, Kyo Bin and Genta-Jouve, Gr{\´e}gory and Huber, Florian and Rogers, Simon and van der Hooft, Justin J. J.}, title = {Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches}, series = {Natural Product Reports}, volume = {38}, journal = {Natural Product Reports}, number = {11}, publisher = {The Royal Society of Chemistry}, issn = {1460-4752}, doi = {10.1039/D1NP00023C}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34772}, pages = {1967 -- 1993}, year = {2021}, language = {en} } @article{HuberStrehleSchnaussetal.2015, author = {Huber, Florian and Strehle, Dan and Schnauß, J{\"o}rg and K{\"a}s, Josef}, title = {Formation of regularly spaced networks as a general feature of actin bundle condensation by entropic forces}, series = {New Journal of Physics}, volume = {17}, journal = {New Journal of Physics}, number = {4}, publisher = {IOP Publishing}, issn = {1367-2630}, doi = {10.1088/1367-2630/17/4/043029}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34833}, year = {2015}, language = {en} } @article{HuberVerhoevenMeijeretal.2020, author = {Huber, Florian and Verhoeven, Stefan and Meijer, Christiaan and Spreeuw, Hanno and Castilla, Efra{\´i}n and Geng, Cunliang and van der Hooft, Justin J. J. and Rogers, Simon and Belloum, Adam and Diblen, Faruk and Spaaks, Jurriaan H.}, title = {matchms - processing and similarity evaluation of mass spectrometry data}, series = {Journal of Open Source Software}, volume = {5}, journal = {Journal of Open Source Software}, number = {52}, publisher = {Cold Spring Harbor Laboratory}, issn = {2475-9066}, doi = {10.21105/joss.02411}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34856}, pages = {2411}, year = {2020}, language = {en} } @article{HuberKaesStuhrmann2008, author = {Huber, Florian and K{\"a}s, Josef and Stuhrmann, Bj{\"o}rn}, title = {Growing actin networks form lamellipodium and lamellum by self-assembly}, series = {Biophysical Journal}, volume = {95}, journal = {Biophysical Journal}, number = {12}, publisher = {Biophysical Society}, issn = {1542-0086}, doi = {10.1529/biophysj.108.134817}, pages = {5508 -- 5523}, year = {2008}, abstract = {Many different cell types are able to migrate by formation of a thin actin-based cytoskeletal extension. Recently, it became evident that this extension consists of two distinct substructures, designated lamellipodium and lamellum, which differ significantly in their kinetic and kinematic properties as well as their biochemical composition. We developed a stochastic two-dimensional computer simulation that includes chemical reaction kinetics, G-actin diffusion, and filament transport to investigate the formation of growing actin networks in migrating cells. Model parameters were chosen based on experimental data or theoretical considerations. In this work, we demonstrate the system's ability to form two distinct networks by self-organization. We found a characteristic transition in mean filament length as well as a distinct maximum in depolymerization flux, both within the first 1-2 microm. The separation into two distinct substructures was found to be extremely robust with respect to initial conditions and variation of model parameters. We quantitatively investigated the complex interplay between ADF/cofilin and tropomyosin and propose a plausible mechanism that leads to spatial separation of, respectively, ADF/cofilin- or tropomyosin-dominated compartments. Tropomyosin was found to play an important role in stabilizing the lamellar actin network. Furthermore, the influence of filament severing and annealing on the network properties is explored, and simulation data are compared to existing experimental data.}, language = {en} } @article{HuberKaes2011, author = {Huber, Florian and K{\"a}s, Josef}, title = {Self-regulative organization of the cytoskeleton}, series = {Cytoskeleton}, volume = {68}, journal = {Cytoskeleton}, number = {5}, publisher = {Wiley}, issn = {1949-3592}, doi = {10.1002/cm.20509}, pages = {259 -- 265}, year = {2011}, abstract = {Despite its impressive complexity the cytoskeleton succeeds to persistently organize itself and thus the cells' interior. In contrast to classical man-made machines, much of the cellular organization originates from inherent self-assembly and self-organization allowing a high degree of autonomy for various functional units. Recent experimental and theoretical studies revealed numerous examples of cytoskeleton components that arrange and organize in a self-regulative way. In the present review we want to shortly summarize some of the principle mechanisms that are able to inherently trigger and regulate the cytoskeleton organization. Although taken individually most of these regulative principles are rather simple with intuitively predictable consequences, combinations of two or more of these mechanisms can quickly give rise to very complex, unexpected behavior and might even be able to explain the formation of different functional units out of a common pool of available building blocks.}, language = {en} } @article{StuhrmannHuberKaes2011, author = {Stuhrmann, Bj{\"o}rn and Huber, Florian and K{\"a}s, Josef}, title = {Robust organizational principles of protrusive biopolymer networks in migrating living cells}, series = {Plos One}, volume = {6}, journal = {Plos One}, number = {1}, publisher = {Public Library of Science (PLoS)}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014471}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34901}, year = {2011}, abstract = {Cell migration is associated with the dynamic protrusion of a thin actin-based cytoskeletal extension at the cell front, which has been shown to consist of two different substructures, the leading lamellipodium and the subsequent lamellum. While the formation of the lamellipodium is increasingly well understood, organizational principles underlying the emergence of the lamellum are just beginning to be unraveled. We report here on a 1D mathematical model which describes the reaction-diffusion processes of a polarized actin network in steady state, and reproduces essential characteristics of the lamellipodium-lamellum system. We observe a steep gradient in filament lengths at the protruding edge, a local depolymerization maximum a few microns behind the edge, as well as a differential dominance of the network destabilizer ADF/cofilin and the stabilizer tropomyosin. We identify simple and robust organizational principles giving rise to the derived network characteristics, uncoupled from the specifics of any molecular implementation, and thus plausibly valid across cell types. An analysis of network length dependence on physico-chemical system parameters implies that to limit array treadmilling to cellular dimensions, network growth has to be truncated by mechanisms other than aging-induced depolymerization, e.g., by myosin-associated network dissociation at the transition to the cell body. Our work contributes to the analytical understanding of the cytoskeletal extension's bisection into lamellipodium and lamellum and sheds light on how cells organize their molecular machinery to achieve motility.}, language = {en} } @article{LangmannRojasPena2016, author = {Langmann, Reinhard and Rojas-Pe{\~n}a, Leandro}, title = {PLCs as Industry 4.0 Components in Laboratory Applications}, series = {International Journal of Online Engineering}, volume = {12}, journal = {International Journal of Online Engineering}, number = {7}, publisher = {iJOE}, issn = {1861-2121}, doi = {10.3991/ijoe.v12i07.5828}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-28089}, pages = {37}, year = {2016}, language = {en} } @article{LangmannStiller2015, author = {Langmann, Reinhard and Stiller, Michael}, title = {Industrial Cloud - Status und Ausblick}, series = {HMD Praxis der Wirtschaftsinformatik}, volume = {52}, journal = {HMD Praxis der Wirtschaftsinformatik}, number = {5}, publisher = {Springer Nature}, doi = {10.1365/s40702-015-0162-0}, pages = {647 -- 664}, year = {2015}, language = {de} } @article{Langmann2010, author = {Langmann, Reinhard}, title = {Distributed Web-Based Control System}, series = {International Journal of Online Engineering (iJOE)}, volume = {6}, journal = {International Journal of Online Engineering (iJOE)}, number = {3}, publisher = {iJOE}, doi = {10.3991/ijoe.v6i3.1345}, year = {2010}, language = {en} } @article{LyalinaLangmannKrisilov2011, author = {Lyalina, Yuliya and Langmann, Reinhard and Krisilov, V.}, title = {The Interaction Model in iLearning Environments and its Use in the Smart Lab Concept}, series = {International Journal of Online Engineering}, volume = {7}, journal = {International Journal of Online Engineering}, number = {4}, publisher = {iJOE}, doi = {10.3991/ijoe.v7i4.1793}, year = {2011}, language = {en} } @article{JohanningBraunTimoneyetal.2009, author = {Johanning, M. and Braun, Alexander and Timoney, N. and Elman, V. and Neuhauser, W. and Wunderlich, Chr}, title = {Individual addressing of trapped ions and coupling of motional and spin states using RF radiation}, series = {Physical review letters}, volume = {102}, journal = {Physical review letters}, number = {7}, publisher = {American Physical Society}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.102.073004}, year = {2009}, abstract = {Individual electrodynamically trapped and laser cooled ions are addressed in frequency space using radio-frequency radiation in the presence of a static magnetic field gradient. In addition, an interaction between motional and spin states induced by an rf field is demonstrated employing rf optical double resonance spectroscopy. These are two essential experimental steps towards realizing a novel concept for implementing quantum simulations and quantum computing with trapped ions.}, language = {en} }