The National Institutes of Healths (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body. Multiple laboratories across the United States are collecting tissue s
pecimens from different organs of donors who vary in sex, age, and body size. Integrating and harmonizing the data derived from these samples and mapping them into a common three-dimensional (3D) space is a major challenge. The key to making this possible is a Common Coordinate Framework (CCF), which provides a semantically annotated, 3D reference system for the entire body. The CCF enables contributors to HuBMAP to register specimens and datasets within a common spatial reference system, and it supports a standardized way to query and explore data in a spatially and semantically explicit manner. [...] This paper describes the construction and usage of a CCF for the human body and its reference implementation in HuBMAP. The CCF consists of (1) a CCF Clinical Ontology, which provides metadata about the specimen and donor (the who); (2) a CCF Semantic Ontology, which describes what part of the body a sample came from and details anatomical structures, cell types, and biomarkers (ASCT+B); and (3) a CCF Spatial Ontology, which indicates where a tissue sample is located in a 3D coordinate system. An initial version of all three CCF ontologies has been implemented for the first HuBMAP Portal release. It was successfully used by Tissue Mapping Centers to semantically annotate and spatially register 48 kidney and spleen tissue blocks. The blocks can be queried and explored in their clinical, semantic, and spatial context via the CCF user interface in the HuBMAP Portal.
This report presents the proceedings of the Course on Advanced Accelerator Physics organized by the CERN Accelerator School. The course was held in Trondheim, Norway from 18 to 29 August 2013, in collaboration with the Norwegian University of Science
and Technology. Its syllabus was based on previous courses and in particular on the course held in Berlin 2003 whose proceedings were published as CERN Yellow Report CERN- 2006-002. The field has seen significant advances in recent years and some topics were presented in a new way and other topics were added. The lectures were supplemented with tutorials on key topics and 14 hours of hands on courses on Optics Design and Corrections, RF Measurement Techniques and Beam Instrumentation and Diagnostics. These courses are a key element of the Advanced Level Course.
Non-linear effects in accelerator physics are important for both successful operation of accelerators and during the design stage. Since both of these aspects are closely related, they will be treated together in this overview. Some of the most impor
tant aspects are well described by methods established in other areas of physics and mathematics. The treatment will be focused on the problems in accelerators used for particle physics experiments. Although the main emphasis will be on accelerator physics issues, some of the aspects of more general interest will be discussed. In particular, we demonstrate that in recent years a framework has been built to handle the complex problems in a consistent form, technically superior and conceptually simpler than the traditional techniques. The need to understand the stability of particle beams has substantially contributed to the development of new techniques and is an important source of examples which can be verified experimentally. Unfortunately, the documentation of these developments is often poor or even unpublished, in many cases only available as lectures or conference proceedings.
