Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (pooled CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells and present a framework to power biological discovery with the resulting genotype-phenotype map. We use transcriptional phenotypes to predict the function of poorly-characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena - from RNA processing to differentiation. We leverage this ability to systematically identify the genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene function and cellular behavior.

PERANCANGAN SISTEM INFORMASI BERBASIS APLIKASI DENGAN METODE COSTUMER RELATIONSHIP MANAGEMENT (CRM) PADA BARBERSHOP (STUDI KASUS: SIAN BARBERSHOP)

Currently, technology is relevant to people's lives because people use technology daily for activities, work, transactions and various aspects of life. Information systems have an important role in everything, one of which is for economic growth and also helps provide information to the public easily. Sian Barbershop is engaged in shaving services and requires a good information system, because the most important business processes for Sian Barbershop are Online Booking and administration. The current problem is that Sian Barbershop still uses conventional methods and still uses written records. On the other hand, long queues are one of the factors that make online ordering systems important for customer convenience. The purpose of this writing and design is a new method where online booking will help customers shave their hair at Sian Barbershop and support existing business processes. The information system that will be designed using Adobe Xd is aimed at selling and attracting the attention of MSME customers. In the design methodology, the steps that need to be done in making this information system are mapping information needs, design and construction of information systems. The result of the design is that the information system application that has been designed and designed has fulfilled the booking function (in CRM) in accordance with the indicators that have been made. The design of this information system already has a usability factor where the information system is feasible and can also be implemented for these SMEs.Saat ini teknologi menjadi hal yang relevan dengan kehidupan masyarakat karena keseharian masyarakat menggunakan teknologi untuk beraktifitas , bekerja , bertransaksi dan berbagai aspek hidup. Sistem informasi mempunyai peran penting dalam segala hal salah satunya untuk pertumbuhan ekonomi dan juga membantu memberikan informasi kepada masyarakat dengan mudah. Sian Barbershop bergerak di bidang jasa mencukur dan membutuhkan sistem informasi yang baik, karena proses bisnis yang paling penting untuk Sian Barbershop adalah Booking Online dan administrasi. Permasalahan saat ini , Sian Barbershop masih menggunakan metode konvensional dan masih menggunakan catatan tertulis. Di sisi lain antrian yang cukup panjang menjadi salah satu faktor yang membuat sistem pemesanan daring menjadi penting bagi kenyamanan pelanggan. Tujuan dari penulisan dan perancangan ini adalah metode baru dimana adanya bookingonline ini akan membantu para pelanggan mencukur rambut di Sian Barbershop dan menunjang proses bisnis yang ada. Sistem Informasi yang akan dirancang menggunakan Adobe Xd yang tertuju penjualan dan menarik perhatian costumer UMKM. Dalam Metodologi perancangan , tahap yang perlu dilakukan dalam membuat sistem informasi ini seperti adalah pemetaan kebutuhan informasi, desain dan konstruksi sistem informasi. Hasil dari perancangan adalah aplikasi sistem informasi yang sudah dirancang dan di desain sudah memenuhi fungsi booking (dalam CRM) sesuai dengan indikator yang sudah dibuat. Perancangan sistem informasi ini sudah memiliki faktor usability dimana sistem informasi sudah layak dan juga bisa diimplementasikan ke UMKM ini.

OntoSLAM: An Ontology for Representing Location and Simultaneous Mapping Information for Autonomous Robots

Autonomous robots are playing an important role to solve the Simultaneous Localization and Mapping (SLAM) problem in different domains. To generate flexible, intelligent, and interoperable solutions for SLAM, it is a must to model the complex knowledge managed in these scenarios (i.e., robots characteristics and capabilities, maps information, locations of robots and landmarks, etc.) with a standard and formal representation. Some studies have proposed ontologies as the standard representation of such knowledge; however, most of them only cover partial aspects of the information managed by SLAM solutions. In this context, the main contribution of this work is a complete ontology, called OntoSLAM, to model all aspects related to autonomous robots and the SLAM problem, towards the standardization needed in robotics, which is not reached until now with the existing SLAM ontologies. A comparative evaluation of OntoSLAM with state-of-the-art SLAM ontologies is performed, to show how OntoSLAM covers the gaps of the existing SLAM knowledge representation models. Results show the superiority of OntoSLAM at the Domain Knowledge level and similarities with other ontologies at Lexical and Structural levels. Additionally, OntoSLAM is integrated into the Robot Operating System (ROS) and Gazebo simulator to test it with Pepper robots and demonstrate its suitability, applicability, and flexibility. Experiments show how OntoSLAM provides semantic benefits to autonomous robots, such as the capability of inferring data from organized knowledge representation, without compromising the information for the application and becoming closer to the standardization needed in robotics.

Using dual-network-analyser for communities detecting in dual networks

Background Representations of the relationships among data using networks are widely used in several research fields such as computational biology, medical informatics and social network mining. Recently, complex networks have been introduced to better capture the insights of the modelled scenarios. Among others, dual networks (DNs) consist of mapping information as pairs of networks containing the same set of nodes but with different edges: one, called physical network, has unweighted edges, while the other, called conceptual network, has weighted edges. Results We focus on DNs and we propose a tool to find common subgraphs (aka communities) in DNs with particular properties. The tool, called Dual-Network-Analyser, is based on the identification of communities that induce optimal modular subgraphs in the conceptual network and connected subgraphs in the physical one. It includes the Louvain algorithm applied to the considered case. The Dual-Network-Analyser can be used to study DNs, to find common modular communities. We report results on using the tool to identify communities on synthetic DNs as well as real cases in social networks and biological data. Conclusion The proposed method has been tested by using synthetic and biological networks. Results demonstrate that it is well able to detect meaningful information from DNs.

A Transformation-Based Quantum Physical Synthesis Approach for Nearest-Neighbor Architectures

The physical synthesis concept for quantum circuits, the interaction between synthesis and physical design processes, was first introduced in our previous work. This concept inspires us to propose some techniques that can minimize the number of extra inserted SWAP operations required to run a circuit on a nearest-neighbor architecture. Minimizing the number of SWAP operations potentially decreases the latency and error probability of a quantum circuit. Focusing on this concept, we present a physical synthesis technique based on transformation rules to decrease the number of SWAP operations in nearest-neighbor architectures. After the qubits of a circuit are mapped onto the physical qubits provided by the target architecture, our procedure is fed by this mapping information. Our method uses the obtained placement and scheduling information to apply some transformation rules to the original netlist to decrease the number of extra SWAP gates required for running the circuit on the architecture. We follow two policies in applying a transformation rule, greedy and simulated-annealing-based policies. Simulation results show that the proposed technique decreases the average number of extra SWAP operations by about 20.6% and 24.1% based on greedy and simulated-annealing-based policies, respectively, compared with the best in the literature.

Review of web mapping: eras, trends and directions

Web mapping and the use of geospatial information online have evolved rapidly over the past few decades. Almost everyone in the world uses mapping information, whether or not one realizes it. Almost every mobile phone now has location services and every event and object on the earth has a location. The use of this geospatial location data has expanded rapidly, thanks to the development of the Internet. Huge volumes of geospatial data are available and daily being captured online, and are used in web applications and maps for viewing, analysis, modeling and simulation. This paper reviews the developments of web mapping from the first static online map images to the current highly interactive, multi-sourced web mapping services that have been increasingly moved to cloud computing platforms. The whole environment of web mapping captures the integration and interaction between three components found online, namely, geospatial information, people and functionality. In this paper, the trends and interactions among these components are identified and reviewed in relation to the technology developments. The review then concludes by exploring some of the opportunities and directions. Keywords: web mapping; Web GIS; Internet; online; web services; digital earth; GeoWeb; semantic web; collaborative; development era

Review of web mapping: eras, trends and directions

Web mapping and the use of geospatial information online have evolved rapidly over the past few decades. Almost everyone in the world uses mapping information, whether or not one realizes it. Almost every mobile phone now has location services and every event and object on the earth has a location. The use of this geospatial location data has expanded rapidly, thanks to the development of the Internet. Huge volumes of geospatial data are available and daily being captured online, and are used in web applications and maps for viewing, analysis, modeling and simulation. This paper reviews the developments of web mapping from the first static online map images to the current highly interactive, multi-sourced web mapping services that have been increasingly moved to cloud computing platforms. The whole environment of web mapping captures the integration and interaction between three components found online, namely, geospatial information, people and functionality. In this paper, the trends and interactions among these components are identified and reviewed in relation to the technology developments. The review then concludes by exploring some of the opportunities and directions. Keywords: web mapping; Web GIS; Internet; online; web services; digital earth; GeoWeb; semantic web; collaborative; development era

Extraction of organic chemistry grammar from unsupervised learning of chemical reactions

Humans use different domain languages to represent, explore, and communicate scientific concepts. During the last few hundred years, chemists compiled the language of chemical synthesis inferring a series of “reaction rules” from knowing how atoms rearrange during a chemical transformation, a process called atom-mapping. Atom-mapping is a laborious experimental task and, when tackled with computational methods, requires continuous annotation of chemical reactions and the extension of logically consistent directives. Here, we demonstrate that Transformer Neural Networks learn atom-mapping information between products and reactants without supervision or human labeling. Using the Transformer attention weights, we build a chemically agnostic, attention-guided reaction mapper and extract coherent chemical grammar from unannotated sets of reactions. Our method shows remarkable performance in terms of accuracy and speed, even for strongly imbalanced and chemically complex reactions with nontrivial atom-mapping. It provides the missing link between data-driven and rule-based approaches for numerous chemical reaction tasks.